2QPW

Methyltransferase domain of human PR domain-containing protein 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherObtained via Se-SAD from second crystal (different crystal form) at low resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729822% PEG 5000 MME, 0.2 M Ammonium sulfate, 0.1 M MES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9436.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.462α = 90
b = 51.196β = 90
c = 70.887γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.97770CHESSA1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.795099.70.06334.37.22399923999
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.791.8699.30.30166.42407

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTObtained via Se-SAD from second crystal (different crystal form) at low resolution1.7941.49123051230563199.410.171040.171040.168420.22157RANDOM23.169
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]
-0.81-0.441.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.888
r_dihedral_angle_3_deg14.279
r_dihedral_angle_4_deg8.909
r_dihedral_angle_1_deg5.947
r_scangle_it4.245
r_scbond_it2.835
r_mcangle_it1.815
r_angle_refined_deg1.507
r_mcbond_it1.198
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.888
r_dihedral_angle_3_deg14.279
r_dihedral_angle_4_deg8.909
r_dihedral_angle_1_deg5.947
r_scangle_it4.245
r_scbond_it2.835
r_mcangle_it1.815
r_angle_refined_deg1.507
r_mcbond_it1.198
r_nbtor_refined0.307
r_xyhbond_nbd_refined0.212
r_nbd_refined0.206
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.177
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms1191
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms

Software

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