X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PVTPDB ENTRY 3PVT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293100 mM Na-ADA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.257α = 90
b = 109.062β = 90
c = 305.926γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDRAYONIX MX-3002009-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-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
12.6549.299.90.081106.5107560
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)
2.642.7399.90.547410749

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 3PVT2.6549.2107560536399.910.23570.23410.2673RANDOM54.7614
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]
-0.58-0.841.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.286
r_dihedral_angle_4_deg18.434
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg4.523
r_scangle_it3.052
r_mcangle_it1.801
r_scbond_it1.695
r_mcbond_it1.277
r_angle_refined_deg1.059
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.286
r_dihedral_angle_4_deg18.434
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg4.523
r_scangle_it3.052
r_mcangle_it1.801
r_scbond_it1.695
r_mcbond_it1.277
r_angle_refined_deg1.059
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24587
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
HKL-2000data reduction