X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HVMPDB ENTRY 2HVM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.411α = 90
b = 112.709β = 90
c = 37.331γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.92098.30.0893.424548
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)
11.91.9798.80.4333.4

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 2HVM1.9202400951398.30.1990.1980.259RANDOM13.24
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]
-0.65-0.260.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.755
r_dihedral_angle_3_deg12.37
r_dihedral_angle_1_deg7.229
r_dihedral_angle_4_deg4.898
r_scangle_it2.91
r_scbond_it2.101
r_angle_refined_deg1.503
r_mcangle_it1.358
r_mcbond_it0.867
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.755
r_dihedral_angle_3_deg12.37
r_dihedral_angle_1_deg7.229
r_dihedral_angle_4_deg4.898
r_scangle_it2.91
r_scbond_it2.101
r_angle_refined_deg1.503
r_mcangle_it1.358
r_mcbond_it0.867
r_nbtor_refined0.31
r_symmetry_hbond_refined0.264
r_nbd_refined0.206
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.143
r_chiral_restr0.105
r_bond_refined_d0.016
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_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 Atoms2159
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing