2QJ9 | pdb_00002qj9

Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1REWpdb entry 1REW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82980.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.961α = 90
b = 105.961β = 90
c = 96.789γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9796BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4434.6899.20.0460.04613.84.112278322783
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.5393.20.3390.3393.33.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1REW2.4430.592374321585116099.050.199760.197060.20.253380.26RANDOM87.859
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.597
r_dihedral_angle_4_deg22.858
r_dihedral_angle_3_deg19.068
r_dihedral_angle_1_deg6.457
r_scangle_it2.783
r_scbond_it1.816
r_angle_refined_deg1.535
r_mcangle_it1.503
r_mcbond_it0.835
r_symmetry_hbond_refined0.352
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3008
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing