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Crystal Structure of Transcriptional Regulator NMB0573/L-Met Complex from Neisseria Meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 95 mM HEPES-Na, 190 mM Calcium Chloride, 26.6% PEG 400, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.831 α = 90 b = 149.676 β = 106.01 c = 77.671 γ = 90
Symmetry Space Group P 1 21 1
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 2006-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.8 30 99.9 0.183 14.6 11.5 35471 -1.5
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 2.8 2.9 99.4 0.653 1.8 8.1 3499
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2p5v 2.8 30 33226 1751 99.91 0.23164 0.22762 0.30578 0.2284 RANDOM 59.889
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] 5.84 11.07 -3.9 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.831 r_dihedral_angle_3_deg 15.43 r_dihedral_angle_4_deg 15.246 r_scangle_it 8.057 r_scbond_it 5.427 r_dihedral_angle_1_deg 5.225 r_mcangle_it 5.106 r_mcbond_it 3.247 r_angle_refined_deg 0.996 r_mcbond_other 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.831 r_dihedral_angle_3_deg 15.43 r_dihedral_angle_4_deg 15.246 r_scangle_it 8.057 r_scbond_it 5.427 r_dihedral_angle_1_deg 5.225 r_mcangle_it 5.106 r_mcbond_it 3.247 r_angle_refined_deg 0.996 r_mcbond_other 0.819 r_angle_other_deg 0.803 r_symmetry_vdw_other 0.212 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.187 r_nbd_other 0.18 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.17 r_metal_ion_refined 0.158 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.082 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9844 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing