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Crystal structure of the apo R132K:Y134F:R111L:L121E mutant of cellular retinoic acid-binding protein II at 1.78 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, 25% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.61 α = 106.08 b = 37.169 β = 106.47 c = 60.837 γ = 89.97
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 MAR CCD 165 mm 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.0000 APS 32-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 1.78 55.81 94.5 0.056 18.2 4.1 23232 1 27.1
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 1.78 1.89 95.7 0.181 6.7 4.3 4259
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2G7B 1.78 19.42 23232 2582 96.66 0.18424 0.17873 0.1798 0.234 0.2355 RANDOM 23.063
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 -0.15 -0.25 -0.64 0.22 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.835 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.052 r_scangle_it 2.289 r_mcangle_it 2.222 r_mcbond_it 1.502 r_scbond_it 1.453 r_angle_refined_deg 1.35 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.835 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.052 r_scangle_it 2.289 r_mcangle_it 2.222 r_mcbond_it 1.502 r_scbond_it 1.453 r_angle_refined_deg 1.35 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.271 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling