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lipocalin-type prostaglandin D synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other C2221 MAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295.5 malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.2 α = 90 b = 66.8 β = 90 c = 105.3 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 IMAGE PLATE RIGAKU RAXIS V 2002-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.010 SPring-8 BL45XU
Data Collection Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 56.8 90.9
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 C2221 MAD model 2.1 56.8 16972 16972 922 90.88 0.24509 0.24509 0.24325 0.2459 0.27932 0.2775 RANDOM 35.531
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] -1.35 4.68 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.826 r_scangle_it 4.709 r_scbond_it 3.023 r_mcangle_it 2.355 r_angle_refined_deg 1.48 r_mcbond_it 1.325 r_dihedral_angle_1_deg 1.271 r_nbd_refined 0.271 r_symmetry_vdw_refined 0.252 r_symmetry_hbond_refined 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.826 r_scangle_it 4.709 r_scbond_it 3.023 r_mcangle_it 2.355 r_angle_refined_deg 1.48 r_mcbond_it 1.325 r_dihedral_angle_1_deg 1.271 r_nbd_refined 0.271 r_symmetry_vdw_refined 0.252 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.104 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2425 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing