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CRYSTAL STRUCTURE OF RHOGDI Lys(135,138,141)Tyr MUTANT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KMT PDB ENTRY 1KMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.88 4M NA FORMATE, pH 7.88
Crystal Properties Matthews coefficient Solvent content 4.29 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.308 α = 90 b = 77.308 β = 90 c = 171.659 γ = 120
Symmetry Space Group P 31 2 1
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 IV OSMIC MIRRORS 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.4 50 97.1 0.09 26.1 7.9 23248
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 2.4 2.49 80.8 0.18 6.44 3.6
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 1KMT 2.4 66.96 22152 1056 97 0.18 0.178 0.1813 0.222 0.222 RANDOM 32.12
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] 1.08 0.54 1.08 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.392 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_3_deg 13.872 r_dihedral_angle_1_deg 6.061 r_angle_refined_deg 2.264 r_scangle_it 1.74 r_angle_other_deg 1.402 r_scbond_it 1.263 r_mcangle_it 0.805 r_mcbond_it 0.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.392 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_3_deg 13.872 r_dihedral_angle_1_deg 6.061 r_angle_refined_deg 2.264 r_scangle_it 1.74 r_angle_other_deg 1.402 r_scbond_it 1.263 r_mcangle_it 0.805 r_mcbond_it 0.753 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.17 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_other 0.154 r_nbd_other 0.152 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.095 r_nbtor_other 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2238 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing