X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P3WPDB ENTRY 1P3W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529515% PEG 6000, 0.1M Bicine pH 8.5, vapor diffusion, sitting drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.776α = 90
b = 99.197β = 90
c = 118.068γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-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
12.055093.50.06814.65.752419
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)
12.052.1266.70.4193.83690

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 1P3W2.055052318268393.450.20.1980.238RANDOM39.009
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]
-1.82-1.433.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.665
r_dihedral_angle_3_deg17.29
r_dihedral_angle_4_deg17.133
r_dihedral_angle_1_deg5.894
r_scangle_it3.573
r_scbond_it2.078
r_angle_refined_deg1.414
r_mcangle_it1.128
r_mcbond_it0.694
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.665
r_dihedral_angle_3_deg17.29
r_dihedral_angle_4_deg17.133
r_dihedral_angle_1_deg5.894
r_scangle_it3.573
r_scbond_it2.078
r_angle_refined_deg1.414
r_mcangle_it1.128
r_mcbond_it0.694
r_nbtor_refined0.3
r_nbd_refined0.195
r_xyhbond_nbd_refined0.152
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.139
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6143
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms30

Software

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