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Crystal structure of dihydrodipicolinate reductase from bartonella henselae at 2.0A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARZ pdb entry 1arz modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 PROPLEX SCREEN: 100MM SODIUM CITRATE PH 5.5, 5% PEG 4000, 200MM SODIUM ACETATE, BAHEA.00189.A AT 6.05MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 4.27 71.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.38 α = 90 b = 109.38 β = 90 c = 176.95 γ = 90
Symmetry Space Group P 43 2 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 ADSC QUANTUM 210 2009-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9744 ALS 5.0.1
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 2.3 20 99.8 0.11 19.94 9.6 48383 48383 -3 32.45
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 2.3 2.36 100 0.618 3.8 8.9 3521
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1arz modified with ccp4 program chainsaw 2.3 20 48501 48332 2444 100 0.179 0.177 0.208 0.1765 RANDOM 18.06
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] -0.06 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.071 r_dihedral_angle_3_deg 13.803 r_dihedral_angle_4_deg 12.894 r_dihedral_angle_1_deg 6.196 r_scangle_it 4.483 r_scbond_it 2.787 r_mcangle_it 1.862 r_angle_refined_deg 1.589 r_mcbond_it 0.957 r_angle_other_deg 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.071 r_dihedral_angle_3_deg 13.803 r_dihedral_angle_4_deg 12.894 r_dihedral_angle_1_deg 6.196 r_scangle_it 4.483 r_scbond_it 2.787 r_mcangle_it 1.862 r_angle_refined_deg 1.589 r_mcbond_it 0.957 r_angle_other_deg 0.954 r_mcbond_other 0.192 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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 3984 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 56
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling