2QJA | pdb_00002qja

Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B12


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
2.9157.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.74α = 90
b = 105.74β = 90
c = 97.61γ = 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
12.5534.6198.90.0620.06210.54.221996719967
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)
12.552.6590.90.4990.4992.43.31

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 1REW2.624.58190711808998199.60.215690.213550.220.254090.26RANDOM77.54
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]
-1.27-0.63-1.271.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.496
r_dihedral_angle_3_deg19.183
r_dihedral_angle_4_deg18.01
r_dihedral_angle_1_deg7.85
r_scangle_it3.249
r_scbond_it2.135
r_angle_refined_deg1.9
r_mcangle_it1.706
r_mcbond_it0.953
r_nbtor_refined0.334
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2993
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing