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Apo form crystal structure of human Lipocalin PGDS .
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.05M Potassium thiocyanate, 30%PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 1.88 34.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.27 α = 90 b = 56.5 β = 90 c = 72.529 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 PIXEL DECTRIS PILATUS 2M 2016-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000030 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 56.5 99.9 0.039 0.999 2.13 4.8 26866
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 91.5 0.465 0.372 2.1 3
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 4IMN 1.45 44.57 25435 1380 98.88 0.17809 0.17625 0.2109 0.208 RANDOM 20.528
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] 0.28 -0.44 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.883 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 13.971 r_long_range_B_refined 8.034 r_dihedral_angle_1_deg 6.764 r_scbond_it 4.329 r_mcangle_it 4.014 r_mcbond_it 2.924 r_angle_refined_deg 2.521 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.883 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 13.971 r_long_range_B_refined 8.034 r_dihedral_angle_1_deg 6.764 r_scbond_it 4.329 r_mcangle_it 4.014 r_mcbond_it 2.924 r_angle_refined_deg 2.521 r_chiral_restr 0.174 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing SCALA data scaling PHASER phasing iMOSFLM data reduction