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Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (hexagonal crystal form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.613 α = 90 b = 155.613 β = 90 c = 116.189 γ = 120
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 MARMOSAIC 225 mm CCD 2005-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97950 ESRF BM14
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 1.9 30 100 0.154 31.2 27.4 126653 -1.5 19.6
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 1.9 1.97 99.9 0.758 3.2 15.5 12608
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 29.88 120095 6478 99.07 0.1678 0.16574 0.1659 0.20629 0.1935 RANDOM 24.636
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] -14.07 -14.07 28.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 18.133 r_dihedral_angle_3_deg 15.644 r_dihedral_angle_1_deg 5.6 r_scangle_it 5.257 r_scbond_it 4.018 r_mcangle_it 2.751 r_mcbond_it 1.769 r_angle_refined_deg 1.077 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.857 r_dihedral_angle_4_deg 18.133 r_dihedral_angle_3_deg 15.644 r_dihedral_angle_1_deg 5.6 r_scangle_it 5.257 r_scbond_it 4.018 r_mcangle_it 2.751 r_mcbond_it 1.769 r_angle_refined_deg 1.077 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10893 Nucleic Acid Atoms Solvent Atoms 801 Heterogen Atoms 12
Software Software Software Name Purpose SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling