X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PP9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES pH 6.5 0.2 M ammonium sulfate 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.652.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.714α = 89.945
b = 77.826β = 90.043
c = 108.99γ = 89.991
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.4152097.90.0810.09915.22.859578
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.510.4410.5453.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3PP92.41519.89959578291296.9580.2130.21140.245434.404
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]
1.6570.287-0.235-0.040.424-1.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.782
r_dihedral_angle_4_deg18.011
r_dihedral_angle_3_deg15.898
r_dihedral_angle_1_deg6.176
r_lrange_it5.357
r_lrange_other5.31
r_scangle_it3.309
r_scangle_other3.309
r_mcangle_it2.886
r_mcangle_other2.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.782
r_dihedral_angle_4_deg18.011
r_dihedral_angle_3_deg15.898
r_dihedral_angle_1_deg6.176
r_lrange_it5.357
r_lrange_other5.31
r_scangle_it3.309
r_scangle_other3.309
r_mcangle_it2.886
r_mcangle_other2.885
r_scbond_it1.938
r_scbond_other1.937
r_mcbond_it1.711
r_mcbond_other1.71
r_angle_refined_deg1.414
r_chiral_restr_other1.232
r_angle_other_deg1.225
r_nbd_other0.221
r_nbd_refined0.173
r_symmetry_nbd_other0.173
r_xyhbond_nbd_refined0.162
r_nbtor_refined0.157
r_symmetry_xyhbond_nbd_refined0.153
r_symmetry_nbd_refined0.133
r_symmetry_xyhbond_nbd_other0.087
r_symmetry_nbtor_other0.073
r_ncsr_local_group_180.07
r_ncsr_local_group_20.069
r_chiral_restr0.067
r_ncsr_local_group_140.067
r_ncsr_local_group_170.064
r_ncsr_local_group_150.063
r_ncsr_local_group_240.057
r_ncsr_local_group_10.056
r_ncsr_local_group_60.056
r_ncsr_local_group_280.056
r_ncsr_local_group_90.054
r_ncsr_local_group_210.054
r_ncsr_local_group_50.053
r_ncsr_local_group_230.053
r_ncsr_local_group_270.053
r_ncsr_local_group_120.052
r_ncsr_local_group_160.052
r_ncsr_local_group_200.052
r_ncsr_local_group_80.051
r_ncsr_local_group_130.049
r_ncsr_local_group_100.048
r_ncsr_local_group_260.048
r_ncsr_local_group_30.037
r_ncsr_local_group_40.037
r_ncsr_local_group_110.033
r_ncsr_local_group_190.033
r_ncsr_local_group_70.032
r_ncsr_local_group_250.031
r_ncsr_local_group_220.028
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10302
Nucleic Acid Atoms
Solvent Atoms537
Heterogen Atoms280

Software

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