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Crystal structure of amidohydrolase pmi1525 (target efi-500319) from proteus mirabilis hi4320
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M SODIUM CACODYLATE, PH 6.5, 0.2M AMMONIUM SULFATE, 30% PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.39 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.203 α = 90 b = 101.203 β = 90 c = 65.614 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 MIRRORS 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.53 90 99.7 0.064 9.9 17.7 58633 -5 20.742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.53 1.56 95 0.8 2.2 15.3
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 3HTW 1.53 50 56733 1795 99.88 0.12095 0.11977 0.1265 0.15637 0.162 RANDOM 28.575
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] -1.4 -0.7 -1.4 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_4_deg 9.812 r_scangle_it 9.321 r_scbond_it 7.078 r_mcangle_it 5.876 r_dihedral_angle_1_deg 5.404 r_mcbond_it 4.4 r_rigid_bond_restr 2.91 r_angle_refined_deg 1.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_4_deg 9.812 r_scangle_it 9.321 r_scbond_it 7.078 r_mcangle_it 5.876 r_dihedral_angle_1_deg 5.404 r_mcbond_it 4.4 r_rigid_bond_restr 2.91 r_angle_refined_deg 1.227 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2817 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 34
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling