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11-BETA DEHYDROGENASE ISOZYME 1 IN COMPLEX WITH COLLETOIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 THE 4 UL DROP CONTAINED 2 UL PROTEIN
(25 MM TRIS, PH 8.0, 250 MM NACL, 4 MM CHAPS, 10 MG/ML PROTEIN)
AND 2 UL WELL SOLUTION (100 MM MES, PH 6.5, 20 PEG 4000), VAPOR
DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.022 α = 90 b = 153.749 β = 93.24 c = 74.051 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 CCD MARMOSAIC 300 mm CCD 2014-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.6 76.87 98.5 0.038 2 5.6 38505 -3
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 2.6 2.69 89.9 0.613 5.1
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3D5Q 2.6 76.87 36549 1930 98.3 0.215 0.213 0.264 0.2745 RANDOM 93.48
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] 6.74 -3.11 -2.77 -3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 13.863 r_long_range_B_refined 11.594 r_long_range_B_other 11.594 r_scangle_other 9.822 r_mcangle_it 7.755 r_mcangle_other 7.755 r_scbond_it 6.696 r_scbond_other 6.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 13.863 r_long_range_B_refined 11.594 r_long_range_B_other 11.594 r_scangle_other 9.822 r_mcangle_it 7.755 r_mcangle_other 7.755 r_scbond_it 6.696 r_scbond_other 6.695 r_dihedral_angle_1_deg 5.671 r_mcbond_it 5.265 r_mcbond_other 5.265 r_angle_refined_deg 1.356 r_angle_other_deg 0.938 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 7128 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 264
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement