3VLA | pdb_00003vla

Crystal structure of edgp


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4950.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.102α = 90
b = 130.102β = 90
c = 44.544γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152008-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
10.9250272047

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMIRTHROUGHOUT0.95202396791270693.440.128470.127560.13730.145590.1539RANDOM10.163
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.265
r_sphericity_free19.027
r_dihedral_angle_4_deg17.325
r_dihedral_angle_3_deg10.616
r_sphericity_bonded7.984
r_dihedral_angle_1_deg6.388
r_rigid_bond_restr3.504
r_angle_refined_deg1.776
r_angle_other_deg1.045
r_chiral_restr0.121
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3061
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement