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Crystal structure of the R132K:R111L:T54E mutant of cellular retinoic acid-binding protein II at 1.85 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G7B PDB entry 2G7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M BTP, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.803 α = 75.52 b = 36.678 β = 74.88 c = 56.892 γ = 88.4
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 300 mm CCD 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97850 APS 21-ID-G
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 1.85 53.2 84.5 0.051 26.6 2.4 18943 1 38.2
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 1.85 1.92 43.3 0.297 2.4 1.7 959
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 (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 PDB entry 2G7B 1.85 35.49 17972 969 84.57 0.19278 0.19278 0.18974 0.2049 0.24847 0.2581 RANDOM 24.122
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] -1.46 -0.21 0.8 -2.63 1.19 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.172 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_4_deg 9.863 r_dihedral_angle_1_deg 5.493 r_mcangle_it 1.38 r_angle_refined_deg 1.238 r_scangle_it 1.06 r_mcbond_it 0.899 r_scbond_it 0.792 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.172 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_4_deg 9.863 r_dihedral_angle_1_deg 5.493 r_mcangle_it 1.38 r_angle_refined_deg 1.238 r_scangle_it 1.06 r_mcbond_it 0.899 r_scbond_it 0.792 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.234 r_nbd_refined 0.229 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling