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CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUCINE 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 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.389 α = 90 b = 149.771 β = 105.68 c = 77.845 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 2.9 30 91.2 0.143 6.3 2.7 28887 -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 2.9 3 63.2 0.386 1.3 2.1 2007
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 MOLECULAR REPLACEMENT THROUGHOUT 2p5v 2.9 30 28166 1454 92.72 0.23853 0.23534 0.2423 0.30008 0.2272 RANDOM 48.167
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] 4.3 11.39 -2.29 4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_3_deg 16.131 r_dihedral_angle_4_deg 15.649 r_scangle_it 9.229 r_scbond_it 6.15 r_mcangle_it 5.791 r_dihedral_angle_1_deg 4.825 r_mcbond_it 3.576 r_angle_refined_deg 1.054 r_mcbond_other 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_3_deg 16.131 r_dihedral_angle_4_deg 15.649 r_scangle_it 9.229 r_scbond_it 6.15 r_mcangle_it 5.791 r_dihedral_angle_1_deg 4.825 r_mcbond_it 3.576 r_angle_refined_deg 1.054 r_mcbond_other 0.888 r_angle_other_deg 0.798 r_symmetry_vdw_other 0.275 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.2 r_nbd_other 0.195 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.161 r_metal_ion_refined 0.157 r_nbtor_other 0.084 r_chiral_restr 0.057 r_xyhbond_nbd_other 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9844 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing