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Crystal Structure of AhQnr, the Qnr protein from Aeromonas hydrophila (P21212 crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PSS PDB ENTRY 3PSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 291 0.1M sodium cacodylate, 1.5M sodium acetate, 20mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.73 α = 90 b = 116.29 β = 90 c = 55.1 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 225 mm CCD 2008-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.117 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 43.43 98.1 0.132 8 4.4 29576 28777 22.162
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) 2.2 2.32 98.6 0.424 3.1 4.3 4050
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 PDB ENTRY 3PSS 2.2 41.45 27321 1455 97.33 0.21379 0.21085 0.2108 0.2699 0.2729 RANDOM 16.51
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] 2.16 -2.51 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_4_deg 13.721 r_dihedral_angle_1_deg 6.324 r_scangle_it 2.5 r_scbond_it 1.588 r_angle_refined_deg 1.364 r_mcangle_it 0.852 r_angle_other_deg 0.845 r_mcbond_it 0.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_4_deg 13.721 r_dihedral_angle_1_deg 6.324 r_scangle_it 2.5 r_scbond_it 1.588 r_angle_refined_deg 1.364 r_mcangle_it 0.852 r_angle_other_deg 0.845 r_mcbond_it 0.466 r_mcbond_other 0.123 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3394 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 91
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling