X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ORV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310% PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Cacodilate pH 6.25
Crystal Properties
Matthews coefficientSolvent content
2.7755.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.357α = 90
b = 117.212β = 105.57
c = 163.396γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99997SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.943.5990.169.54.2895096
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0999.20.944.984.38

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ORV2.943.5290340475599.020.268520.265230.33173RANDOM38.595
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]
-3.15-0.073.76-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.439
r_dihedral_angle_4_deg15.501
r_dihedral_angle_3_deg15.44
r_dihedral_angle_1_deg6.538
r_long_range_B_refined4.858
r_long_range_B_other4.858
r_mcangle_it2.705
r_mcangle_other2.705
r_scangle_other2.272
r_angle_other_deg1.985
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.439
r_dihedral_angle_4_deg15.501
r_dihedral_angle_3_deg15.44
r_dihedral_angle_1_deg6.538
r_long_range_B_refined4.858
r_long_range_B_other4.858
r_mcangle_it2.705
r_mcangle_other2.705
r_scangle_other2.272
r_angle_other_deg1.985
r_mcbond_it1.531
r_mcbond_other1.531
r_angle_refined_deg1.335
r_scbond_it1.273
r_scbond_other1.273
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26248
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing