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The Crystal Structure of Dihydrodipicolinate reductase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil sitting drop 4.5 298 2.0M Ammonium sulfate, 0.2M Sodium actetate , pH 4.5, Microbatch under oil sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.9 α = 90 b = 112.44 β = 90 c = 131.61 γ = 90
Symmetry Space Group P 21 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 CCD MARMOSAIC 225 mm CCD Mirror 2010-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 29.64 98 0.086 0.092 12.7 6.9 115798 2.9 2.9 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 93.4 0.559 0.607 2.9 6.1 97586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1ARZ 1.8 28.5 2 115798 109818 5791 97.63 0.199 0.198 0.2128 0.225 0.2396 RANDOM 30.05
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] 1.31 -0.26 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.251 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 5.509 r_scangle_it 2.076 r_scbond_it 1.257 r_angle_refined_deg 1.046 r_mcangle_it 0.738 r_mcbond_it 0.388 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.251 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 5.509 r_scangle_it 2.076 r_scbond_it 1.257 r_angle_refined_deg 1.046 r_mcangle_it 0.738 r_mcbond_it 0.388 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7495 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 130
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling