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N. meningitidis CMP-sialic acid synthetase in the presence of CMP and Neu5Ac2en
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M sodium citrate/citric acid pH 5.5 and 20% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.48 α = 90 b = 151.01 β = 90 c = 84.9 γ = 90
Symmetry Space Group C 2 2 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 2015-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97950 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.68 97.86 97.1 0.089 0.995 11.57 3.14 22814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.75 94.2 0.503 0.727 2.13 2.78
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 1EYR 2.684 97.86 21689 1118 97.11 0.19673 0.1944 0.1973 0.24171 0.2411 RANDOM 43.447
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] 1.14 -2 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_3_deg 17.699 r_dihedral_angle_4_deg 16.176 r_long_range_B_refined 6.92 r_long_range_B_other 6.92 r_dihedral_angle_1_deg 6.513 r_scangle_other 4.734 r_mcangle_it 4.458 r_mcangle_other 4.458 r_scbond_it 2.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.883 r_dihedral_angle_3_deg 17.699 r_dihedral_angle_4_deg 16.176 r_long_range_B_refined 6.92 r_long_range_B_other 6.92 r_dihedral_angle_1_deg 6.513 r_scangle_other 4.734 r_mcangle_it 4.458 r_mcangle_other 4.458 r_scbond_it 2.959 r_scbond_other 2.957 r_mcbond_other 2.813 r_mcbond_it 2.812 r_angle_refined_deg 1.598 r_angle_other_deg 1.24 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5166 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing