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Crystal structure of para-aminobenzoate synthetase, component I from Cytophaga hutchinsonii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SAD model built using ARP/wARP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 100mM MES pH 6.5 + 25% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.006 α = 90 b = 159.497 β = 90 c = 115.542 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm 2009-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID .97929 APS 31-ID
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 1.56 21.37 96.7 0.072 19.6 14.4 76012 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.56 1.65 78.1 0.43 6.4 12.6 8898
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 SAD THROUGHOUT Built using ARP/wARP 1.57 20.81 75965 3818 100 0.174 0.173 0.1857 0.192 0.2059 RANDOM 22.818
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.32 r_dihedral_angle_4_deg 21.839 r_dihedral_angle_3_deg 12.372 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.968 r_scbond_it 2.086 r_mcangle_it 1.301 r_angle_refined_deg 1.279 r_mcbond_it 0.983 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.32 r_dihedral_angle_4_deg 21.839 r_dihedral_angle_3_deg 12.372 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.968 r_scbond_it 2.086 r_mcangle_it 1.301 r_angle_refined_deg 1.279 r_mcbond_it 0.983 r_angle_other_deg 0.832 r_symmetry_vdw_other 0.211 r_nbd_refined 0.195 r_mcbond_other 0.189 r_nbd_other 0.186 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.134 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_refined 0.109 r_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling HKL2Map phasing