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 12.5 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.9458.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.358α = 90
b = 102.791β = 90
c = 386.422γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2021-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

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
12.3573099.70.050.06139.410.287496
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)
12.362.4498.90.3520.3946.5

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-VALUE3PP92.35729.77887239425999.4770.2240.2230.240433.296
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]
-0.0090.0060.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.256
r_dihedral_angle_3_deg16.341
r_dihedral_angle_4_deg15.961
r_dihedral_angle_1_deg6.234
r_lrange_it6.02
r_lrange_other6.015
r_scangle_it3.953
r_scangle_other3.953
r_mcangle_it3.582
r_mcangle_other3.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.256
r_dihedral_angle_3_deg16.341
r_dihedral_angle_4_deg15.961
r_dihedral_angle_1_deg6.234
r_lrange_it6.02
r_lrange_other6.015
r_scangle_it3.953
r_scangle_other3.953
r_mcangle_it3.582
r_mcangle_other3.581
r_scbond_it2.437
r_scbond_other2.437
r_mcbond_it2.161
r_mcbond_other2.161
r_angle_refined_deg1.42
r_angle_other_deg1.244
r_nbd_other0.292
r_symmetry_nbd_refined0.288
r_symmetry_xyhbond_nbd_refined0.203
r_symmetry_nbd_other0.184
r_nbd_refined0.182
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.151
r_ncsr_local_group_250.079
r_symmetry_nbtor_other0.078
r_ncsr_local_group_150.077
r_ncsr_local_group_40.076
r_ncsr_local_group_190.076
r_ncsr_local_group_50.075
r_ncsr_local_group_100.074
r_ncsr_local_group_30.071
r_ncsr_local_group_270.071
r_ncsr_local_group_70.07
r_ncsr_local_group_10.069
r_ncsr_local_group_230.069
r_ncsr_local_group_140.067
r_ncsr_local_group_200.067
r_ncsr_local_group_180.066
r_ncsr_local_group_280.066
r_ncsr_local_group_210.065
r_ncsr_local_group_240.065
r_symmetry_xyhbond_nbd_other0.064
r_ncsr_local_group_130.064
r_ncsr_local_group_260.064
r_ncsr_local_group_110.062
r_ncsr_local_group_160.062
r_ncsr_local_group_120.06
r_chiral_restr0.059
r_ncsr_local_group_80.059
r_ncsr_local_group_220.059
r_ncsr_local_group_60.053
r_ncsr_local_group_90.053
r_ncsr_local_group_20.051
r_ncsr_local_group_170.035
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9937
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms450

Software

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