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Methyltransferase domain of human PR domain-containing protein 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Obtained via Se-SAD from second crystal (different crystal form) at low resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 22% PEG 5000 MME, 0.2 M Ammonium sulfate, 0.1 M MES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.462 α = 90 b = 51.196 β = 90 c = 70.887 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2007-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97770 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.79 50 99.7 0.063 34.3 7.2 23999 23999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.79 1.86 99.3 0.301 6 6.4 2407
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Obtained via Se-SAD from second crystal (different crystal form) at low resolution 1.79 41.49 12305 12305 631 99.41 0.17104 0.17104 0.16842 0.1683 0.22157 0.2204 RANDOM 23.169
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 -0.44 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_3_deg 14.279 r_dihedral_angle_4_deg 8.909 r_dihedral_angle_1_deg 5.947 r_scangle_it 4.245 r_scbond_it 2.835 r_mcangle_it 1.815 r_angle_refined_deg 1.507 r_mcbond_it 1.198 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_3_deg 14.279 r_dihedral_angle_4_deg 8.909 r_dihedral_angle_1_deg 5.947 r_scangle_it 4.245 r_scbond_it 2.835 r_mcangle_it 1.815 r_angle_refined_deg 1.507 r_mcbond_it 1.198 r_nbtor_refined 0.307 r_xyhbond_nbd_refined 0.212 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.177 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 1191 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing