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Crystal structure of Staphylococcal IMPase-I complex with 3Mg2+ and Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2M MgCl2, 0.1M HEPES pH8,18% (W/V) PEG 3350, Soaked with 0.1M HEPES pH8, 18% (W/V) PEG 3350, 10% Glycerol for 24 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.428 α = 90 b = 62.455 β = 90 c = 140.497 γ = 90
Symmetry Space Group P 21 2 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 IMAGE PLATE RIGAKU RAXIS IV++ mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.503 140.497 97.3 0.149 14.3 7.6 18411 18411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.503 2.64 95.7 0.695 0.695 0.266 1.1 7.7 2588
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QMF 2.503 46.72 18387 953 96.75 0.181 0.1771 0.2569 0.2079 RANDOM 27.592
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] 0.06 0.89 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.309 r_dihedral_angle_4_deg 28.816 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_1_deg 7.735 r_angle_refined_deg 1.807 r_angle_other_deg 0.869 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.309 r_dihedral_angle_4_deg 28.816 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_1_deg 7.735 r_angle_refined_deg 1.807 r_angle_other_deg 0.869 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4191 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction