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Crystal structure of catalytic domain of GLP with MS012
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.429 α = 90 b = 95.9 β = 90 c = 102.113 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 315 2014-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.66 50 100 0.118 0.128 0.049 7.4 6.8 86624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 100 0.883 0.789 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3K5K 1.66 50.01 84739 1745 99.85 0.1711 0.1707 0.1798 0.1917 0.2008 RANDOM 21.363
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] 0.63 -0.74 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.794 r_dihedral_angle_4_deg 12.638 r_dihedral_angle_3_deg 11.39 r_dihedral_angle_1_deg 5.919 r_mcangle_it 1.951 r_angle_refined_deg 1.448 r_mcbond_it 1.172 r_mcbond_other 1.171 r_angle_other_deg 1.042 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.794 r_dihedral_angle_4_deg 12.638 r_dihedral_angle_3_deg 11.39 r_dihedral_angle_1_deg 5.919 r_mcangle_it 1.951 r_angle_refined_deg 1.448 r_mcbond_it 1.172 r_mcbond_other 1.171 r_angle_other_deg 1.042 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4122 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction Coot model building HKL-3000 data reduction MOLREP phasing