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Structure of CrgA, a LysR-type transcriptional regulator from Neisseria meningitidis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 10% v/v MPD, 0.1M sodium acetate pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.638 α = 90 b = 119.091 β = 90 c = 250.204 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9765 ESRF ID14-4
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 3.2 30 83.8 0.061 17.8 3.7 43934 -1
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 3.2 3.31 85.3 0.512 1.66 2.7
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 3HHF 3.2 29.88 40596 2165 86.45 0.21787 0.21426 0.2284 0.28584 0.2947 RANDOM 70.603
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] -4.2 0.26 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.273 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_4_deg 12.976 r_scangle_it 6.88 r_dihedral_angle_1_deg 5.733 r_mcangle_it 4.321 r_scbond_it 4.105 r_mcbond_it 2.379 r_angle_refined_deg 0.931 r_angle_other_deg 0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.273 r_dihedral_angle_3_deg 15.07 r_dihedral_angle_4_deg 12.976 r_scangle_it 6.88 r_dihedral_angle_1_deg 5.733 r_mcangle_it 4.321 r_scbond_it 4.105 r_mcbond_it 2.379 r_angle_refined_deg 0.931 r_angle_other_deg 0.789 r_mcbond_other 0.579 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 18304 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling