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Crystal structure of muramidase from Acinetobacter baumannii AB 5075UW prophage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ANV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2M Li2SO4; 0.1M MES pH 6.5; 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.98 α = 90 b = 67 β = 90 c = 75.76 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS 6M-F 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.2 50.18 94.1 0.113 0.126 0.054 0.994 5.6 5 46812
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 94.6 0.929 1.039 0.452 0.762 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 2ANV 1.2 50.18 44084 2373 92.52 0.1485 0.1474 0.1568 0.1685 0.175 RANDOM 17.417
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] -0.51 1.19 -0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.476 r_dihedral_angle_2_deg 31.418 r_dihedral_angle_4_deg 12.027 r_dihedral_angle_3_deg 11.037 r_sphericity_bonded 9.976 r_dihedral_angle_1_deg 5.574 r_rigid_bond_restr 3.195 r_angle_other_deg 2.118 r_angle_refined_deg 1.901 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.476 r_dihedral_angle_2_deg 31.418 r_dihedral_angle_4_deg 12.027 r_dihedral_angle_3_deg 11.037 r_sphericity_bonded 9.976 r_dihedral_angle_1_deg 5.574 r_rigid_bond_restr 3.195 r_angle_other_deg 2.118 r_angle_refined_deg 1.901 r_chiral_restr 0.14 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1139 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 11
Software Software Software Name Purpose HKL-2000 data collection Aimless data scaling MoRDa model building REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing