X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VGBPDB ENTRY 2VGB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.4pH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.550.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.705α = 90
b = 171.164β = 91.61
c = 85.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2000-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.920890.17.21.842512
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9368.60.282.41.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VGB2.87204153385588.70.2580.2570.311RANDOM2
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]
5.55-5.57-1.3-4.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.239
r_dihedral_angle_3_deg23.198
r_dihedral_angle_4_deg23.117
r_dihedral_angle_1_deg6.598
r_angle_refined_deg2.162
r_symmetry_vdw_refined0.491
r_nbtor_refined0.352
r_symmetry_hbond_refined0.329
r_nbd_refined0.311
r_xyhbond_nbd_refined0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.239
r_dihedral_angle_3_deg23.198
r_dihedral_angle_4_deg23.117
r_dihedral_angle_1_deg6.598
r_angle_refined_deg2.162
r_symmetry_vdw_refined0.491
r_nbtor_refined0.352
r_symmetry_hbond_refined0.329
r_nbd_refined0.311
r_xyhbond_nbd_refined0.235
r_chiral_restr0.123
r_scangle_it0.034
r_bond_refined_d0.023
r_scbond_it0.023
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15218
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing