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Native 3-dehydroquinase from Salmonella typhi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFE COMPLEXED 3-DEHYDROQUINASE STRUCTURE SOLVED MIR METHODS (ON HOLD AS 1QFE.PDB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PEG 4000 (1:3, W/V), 100 MM CITRATE-PHOSPHATE PH 5.0 TO 6.5, PRECIPITANT TO BUFFER RATIO >> 4:6 TO 3:7
Crystal Properties Matthews coefficient Solvent content 2.14 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.78 α = 90 b = 112.33 β = 90 c = 42.94 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 277 IMAGE PLATE MARRESEARCH 1994-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 EMBL/DESY, HAMBURG X31
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 1.78 11.75 97.2 0.051 4.12 22422 2
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 1.78 1.86 83 0.038 0.294 3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT COMPLEXED 3-DEHYDROQUINASE STRUCTURE SOLVED MIR METHODS (ON HOLD AS 1QFE.PDB) 1.78 11.75 2 22422 4618 97.2 0.199 0.1721 0.247 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation p_planar_d 0.047 p_angle_d 0.038 p_bond_d 0.018 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr
RMS Deviations Key Refinement Restraint Deviation p_planar_d 0.047 p_angle_d 0.038 p_bond_d 0.018 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr p_chiral_restr p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1934 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing