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Crystal structure of a mammalian reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CYD PDB ENTRY 1CYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.2M sodium acetate, 20%(v/v) glycerol, 0.1M Hepes/NaOH buffer, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.612 α = 90 b = 109.612 β = 90 c = 94.308 γ = 90
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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 40 99.1 0.102 5.3 6.4 176173 13.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 98.1 0.297 2.4 4.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CYD 1.5 40 167340 8816 99 0.162 0.161 0.187 RANDOM 14.51
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.473 r_scangle_it 4.174 r_scbond_it 2.512 r_mcangle_it 1.733 r_angle_refined_deg 1.54 r_mcbond_it 0.929 r_angle_other_deg 0.856 r_symmetry_vdw_refined 0.308 r_symmetry_vdw_other 0.259 r_nbd_other 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.473 r_scangle_it 4.174 r_scbond_it 2.512 r_mcangle_it 1.733 r_angle_refined_deg 1.54 r_mcbond_it 0.929 r_angle_other_deg 0.856 r_symmetry_vdw_refined 0.308 r_symmetry_vdw_other 0.259 r_nbd_other 0.243 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.094 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 7516 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 192
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling