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Crystal structure of 3 residues truncated version of protein NMB1012 from Neisseria meningitides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 20 % PEG 3000, Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.744 α = 90 b = 79.789 β = 105.4 c = 65.605 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 315 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.85 50 99.7 0.075 46.8 7.2 55262 55262 -3
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 1.85 1.87 100 0.475 4.32 6.9 1369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.85 39.8 52424 52424 2811 99.46 0.1983 0.1983 0.19665 0.1954 0.22877 0.2288 RANDOM 31.921
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] 1.95 -0.76 0.67 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.946 r_dihedral_angle_4_deg 15.054 r_dihedral_angle_3_deg 13.784 r_dihedral_angle_1_deg 6.536 r_scangle_it 3.325 r_scbond_it 2.41 r_angle_refined_deg 1.436 r_mcangle_it 1.267 r_mcbond_it 0.962 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.946 r_dihedral_angle_4_deg 15.054 r_dihedral_angle_3_deg 13.784 r_dihedral_angle_1_deg 6.536 r_scangle_it 3.325 r_scbond_it 2.41 r_angle_refined_deg 1.436 r_mcangle_it 1.267 r_mcbond_it 0.962 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.258 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4606 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing