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Crystal Structure of Zebrafish Interphotoreceptor Retinoid-Binding Protein (IRBP) Module 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J7X PDB ENTRY 1J7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 295 Protein solutions at a concentration of 20mg/ml were mixed with the reservoir solutions of 35-44% polyethylene glycol 8000 in 100mM HEPES pH 7.5 buffer containing 100mM NaBr in the 1:1, 2:1 and 3:1 volume ratios and vapor diffused against the reservoir solutions. Plate-shaped crystals appeared in about a week and continued to grow for a few more weeks., VAPOR DIFFUSION, SITTING DROP, temperature 295.K
Crystal Properties Matthews coefficient Solvent content 2.46 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.295 α = 90 b = 97.771 β = 90 c = 41.214 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315 2009-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979368, 0.979484, 0.9716932 APS 19-ID
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 1.9 50 99.6 0.085 40 6.8 27277
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 1.901 1.95 99.8 0.64 2.8 6.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD COMBINED WITH MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1J7X 1.9 50 27277 25467 1332 98.3 0.222 0.219 0.2201 0.268 0.2641 RANDOM 33.4
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] -1.2 2.41 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.262 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_4_deg 12.23 r_dihedral_angle_1_deg 5.711 r_scangle_it 4.008 r_scbond_it 2.51 r_mcangle_it 1.534 r_angle_refined_deg 1.374 r_mcbond_it 0.792 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.262 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_4_deg 12.23 r_dihedral_angle_1_deg 5.711 r_scangle_it 4.008 r_scbond_it 2.51 r_mcangle_it 1.534 r_angle_refined_deg 1.374 r_mcbond_it 0.792 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_other r_long_range_B_refined 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 2338 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 53
Software Software Software Name Purpose ADSC data collection CCP4 model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling CCP4 phasing