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Crystal structure of the human PDI-peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GS3 PDB entry 2gs3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295.15 2.5M ammonium sulfate, 0.1M 2-(N-morpholino)ethanesulfonic acid, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.43 α = 90 b = 122.3 β = 117.9 c = 70.18 γ = 90
Symmetry Space Group C 1 2 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 225 mm CCD 2006-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.89997 EMBL/DESY, HAMBURG X12
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 1.8 66.9 99.3 0.071 16 5 61998 20.7
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) 1.8 1.846 99.3 0.26 5.7 5.1 9242
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 Phaser_MR THROUGHOUT PDB entry 2gs3 1.8 20 58897 3100 99.67 0.21059 0.2086 0.209 0.24811 0.2475 RANDOM 16.184
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] 0.67 0.62 -0.17 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_3_deg 14.724 r_dihedral_angle_4_deg 14.408 r_dihedral_angle_1_deg 5.99 r_scangle_it 3.621 r_scbond_it 2.225 r_mcangle_it 1.414 r_angle_refined_deg 1.352 r_mcbond_it 0.809 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_3_deg 14.724 r_dihedral_angle_4_deg 14.408 r_dihedral_angle_1_deg 5.99 r_scangle_it 3.621 r_scbond_it 2.225 r_mcangle_it 1.414 r_angle_refined_deg 1.352 r_mcbond_it 0.809 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4181 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 5
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling