X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M3V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.15CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 12.0 MG/ML PROTEIN IN 10 MM HEPES PH8.0, 100 MM NACL, 1 MM EDTA, EQUALLY WITH 33.00 %(W/V) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.65α = 90
b = 73.02β = 90
c = 140.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.15PIXELDECTRIS PILATUS3 2M2015-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.883099.50.080.090.0418.54.340305
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.980.6220.7070.332

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 REPLACEMENTTHROUGHOUT5M3V1.883040305197699.350.233290.23130.27247RANDOM56.123
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]
-2.25-1.73.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.24
r_dihedral_angle_3_deg14.379
r_dihedral_angle_4_deg13.904
r_dihedral_angle_1_deg9.593
r_long_range_B_refined8.592
r_long_range_B_other8.309
r_scangle_other1.953
r_mcangle_it1.406
r_mcangle_other1.405
r_angle_refined_deg1.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.24
r_dihedral_angle_3_deg14.379
r_dihedral_angle_4_deg13.904
r_dihedral_angle_1_deg9.593
r_long_range_B_refined8.592
r_long_range_B_other8.309
r_scangle_other1.953
r_mcangle_it1.406
r_mcangle_other1.405
r_angle_refined_deg1.372
r_scbond_it1.312
r_scbond_other1.312
r_angle_other_deg0.855
r_mcbond_it0.851
r_mcbond_other0.851
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3318
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing