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Crystal structure of E. coli PmrD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JSO PDB ENTRY 2JSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 50 mM sodium acetate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.58 α = 90 b = 83.58 β = 90 c = 75.951 γ = 120
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 mirrors 2005-07-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.97959 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 79.6 5617 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 28.1
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 PDB ENTRY 2JSO 2.352 16.81 4370 4111 195 98.15 0.21435 0.21435 0.21109 0.2243 0.28145 0.2925 RANDOM 74.083
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] -0.01 -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_3_deg 24.851 r_dihedral_angle_4_deg 22.512 r_dihedral_angle_1_deg 9.101 r_angle_refined_deg 2.16 r_angle_other_deg 0.978 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_3_deg 24.851 r_dihedral_angle_4_deg 22.512 r_dihedral_angle_1_deg 9.101 r_angle_refined_deg 2.16 r_angle_other_deg 0.978 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 661 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling