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Low resolution structure of Neisseria meningitidis qNOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283.15 PEG 400, cadmium chloride, magnesium chloride, 2-(N-morpholino)ethanesulfonic acid
Crystal Properties Matthews coefficient Solvent content 4.47 72.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.682 α = 90 b = 123.096 β = 90 c = 130.845 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 RAYONIX MX225HE 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 4.2 53.64 99.86 0.251 0.261 0.07 0.998 5.5 14.4 11511 170.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.2 4.7 99.9 7.681 7.954 2.053 0.264 14.9
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 3AYF 4.2 53.64 11004 509 99.78 0.335 0.3333 0.3362 0.3734 0.3659 RANDOM 287.437
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] 7.75 -5.94 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.813 r_dihedral_angle_3_deg 16.45 r_dihedral_angle_4_deg 9.92 r_dihedral_angle_1_deg 7.177 r_angle_refined_deg 1.282 r_angle_other_deg 1.043 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.813 r_dihedral_angle_3_deg 16.45 r_dihedral_angle_4_deg 9.92 r_dihedral_angle_1_deg 7.177 r_angle_refined_deg 1.282 r_angle_other_deg 1.043 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 88
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing