2VXZ

Crystal Structure of hypothetical protein PyrSV_gp04 from Pyrobaculum spherical virus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.51.8M NACL, 0.112M KH2PI, 0.112M NAH2PI, 0.1M MES, PH6.5
Crystal Properties
Matthews coefficientSolvent content
1.9336

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.753α = 90
b = 46.654β = 90
c = 81.363γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q4RMIRROR2007-04-30MMAD
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
11.73099.10.7611.572.76163183
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)
11.71.899.10.512.262.71

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 DIFFRACTIONMADTHROUGHOUTNONE1.728.431631887199.60.1850.1830.227RANDOM19.65
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]
0.07-0.140.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_4_deg18.669
r_dihedral_angle_3_deg13.049
r_dihedral_angle_1_deg4.491
r_scangle_it3.071
r_scbond_it2.222
r_angle_refined_deg1.131
r_mcangle_it1.13
r_mcbond_it1.036
r_angle_other_deg0.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_4_deg18.669
r_dihedral_angle_3_deg13.049
r_dihedral_angle_1_deg4.491
r_scangle_it3.071
r_scbond_it2.222
r_angle_refined_deg1.131
r_mcangle_it1.13
r_mcbond_it1.036
r_angle_other_deg0.845
r_symmetry_vdw_other0.219
r_nbd_refined0.207
r_symmetry_hbond_refined0.189
r_nbd_other0.183
r_nbtor_refined0.177
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.148
r_nbtor_other0.082
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
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 Atoms1229
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing