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Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2 (HSDL2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E03 3E03.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG 3350, 0.1M BIS-TRIS pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.149 α = 90 b = 78.332 β = 90 c = 121.765 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX-300 2009-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97959 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 48.07 99.9 0.11 0.11 9.4 4.4 28262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 99.8 0.895 0.895 2 4.4 17872
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3E03.pdb 2.25 48.07 26820 26820 1441 99.49 0.20187 0.20187 0.19948 0.2071 0.24679 0.255 RANDOM 15.678
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] 3.44 -1.99 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.583 r_dihedral_angle_4_deg 16.853 r_dihedral_angle_3_deg 14.939 r_dihedral_angle_1_deg 5.866 r_scangle_it 2.501 r_scbond_it 1.579 r_angle_refined_deg 1.442 r_angle_other_deg 0.905 r_mcangle_it 0.876 r_mcbond_it 0.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.583 r_dihedral_angle_4_deg 16.853 r_dihedral_angle_3_deg 14.939 r_dihedral_angle_1_deg 5.866 r_scangle_it 2.501 r_scbond_it 1.579 r_angle_refined_deg 1.442 r_angle_other_deg 0.905 r_mcangle_it 0.876 r_mcbond_it 0.481 r_mcbond_other 0.108 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4078 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 142
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling