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Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (kdsC) from Moraxella catarrhalis in complex with Magnesium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N1U PDB ENTRY 3N1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 100 MM MG FORMATE, 100 MM BIS-TRIS PROPANE (PH 5.0), 28% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.264 α = 90 b = 43.562 β = 91.18 c = 87.552 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 IMAGE PLATE MARRESEARCH MIRROR 2013-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H
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 1.64 50 99.8 0.05 22.3 3.9 92882 2
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 1.64 1.67 99.5 0.43 2.32 3.6
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 PDB ENTRY 3N1U 1.64 27.16 76193 4009 99.82 0.19857 0.19698 0.195 0.22831 0.2276 RANDOM 21.394
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] -0.2 -0.33 0.75 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 17.215 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 4.606 r_angle_refined_deg 0.91 r_mcangle_it 0.596 r_scbond_it 0.438 r_mcbond_it 0.336 r_chiral_restr 0.064 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 17.215 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 4.606 r_angle_refined_deg 0.91 r_mcangle_it 0.596 r_scbond_it 0.438 r_mcbond_it 0.336 r_chiral_restr 0.064 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5282 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing