X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PVHPDB ENTRY 1PVH CHAIN B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.5M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
7.86610184.363281

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 193.476α = 90
b = 240.131β = 90
c = 202.631γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.968APS22-ID

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
142094.20.2266.36.63710437104
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)
144.1472.50.8571

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PVH CHAIN B4200.8573523935239185293.630.239780.239780.237240.28696RANDOM102.084
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]
10.49-2.61-7.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.188
r_dihedral_angle_3_deg24.328
r_dihedral_angle_4_deg20.222
r_dihedral_angle_1_deg8.334
r_scangle_it1.77
r_angle_refined_deg1.739
r_scbond_it1.02
r_mcangle_it0.964
r_mcbond_it0.527
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.188
r_dihedral_angle_3_deg24.328
r_dihedral_angle_4_deg20.222
r_dihedral_angle_1_deg8.334
r_scangle_it1.77
r_angle_refined_deg1.739
r_scbond_it1.02
r_mcangle_it0.964
r_mcbond_it0.527
r_nbtor_refined0.327
r_nbd_refined0.279
r_symmetry_vdw_refined0.235
r_xyhbond_nbd_refined0.204
r_symmetry_hbond_refined0.133
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10252
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms587

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing