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Reductase domain of the carboxylate reductase of Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 Crystals were grown by mixing 0.5 microL 0.2 M ammonia sulphate, 0.1 M BisTRIS pH 5.5 and 25 percent PEG 3350 with 0.5 microL 18.00 mg per mL NcCAR R-domain in 50 mM MES buffer pH pH 7.0 containing 10 mM magnesium chloride, 150 mM sodium chloride and 1 mM DTT. Crystals appeared after 6-9 weeks under vapor batch conditions.
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.235 α = 90 b = 137.487 β = 112.333 c = 66.513 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 PIXEL DECTRIS PILATUS 2M 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.3 48.651 99.7 0.191 0.257 0.171 0.98 5.8 3.8 41333
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 2.3 2.38 0.704 0.949 0.631 0.636 3.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MSP 2.3 48.651 41299 2039 99.614 0.203 0.2002 0.2023 0.2586 0.2602 26.121
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] 0.551 -1.231 0.075 0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.216 r_dihedral_angle_4_deg 19.938 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_1_deg 7.018 r_lrange_it 6.997 r_lrange_other 6.862 r_scangle_it 4.608 r_scangle_other 4.603 r_mcangle_it 3.915 r_mcangle_other 3.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.216 r_dihedral_angle_4_deg 19.938 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_1_deg 7.018 r_lrange_it 6.997 r_lrange_other 6.862 r_scangle_it 4.608 r_scangle_other 4.603 r_mcangle_it 3.915 r_mcangle_other 3.915 r_scbond_it 2.769 r_scbond_other 2.764 r_mcbond_it 2.428 r_mcbond_other 2.427 r_angle_refined_deg 1.486 r_angle_other_deg 1.267 r_symmetry_xyhbond_nbd_refined 0.327 r_nbd_other 0.246 r_symmetry_nbd_refined 0.196 r_nbd_refined 0.193 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.153 r_ncsr_local_group_1 0.085 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6206 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing Coot model building