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The crystal structure of human RRAD in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel swissmodel (first approach mode)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.15M sodium malate,
20% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.427 α = 90 b = 58.56 β = 97.18 c = 53.603 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.9 24816
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 1.9 1.97 100
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 swissmodel (first approach mode) 1.9 39.4 23536 23536 1266 99.18 0.19726 0.19726 0.19512 0.2006 0.23538 0.237 RANDOM 28.238
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] 0.11 -0.61 1.53 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.476 r_dihedral_angle_4_deg 17.429 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.466 r_scbond_it 2.28 r_angle_refined_deg 1.605 r_mcangle_it 1.535 r_mcbond_it 1.01 r_angle_other_deg 0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.476 r_dihedral_angle_4_deg 17.429 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.466 r_scbond_it 2.28 r_angle_refined_deg 1.605 r_mcangle_it 1.535 r_mcbond_it 1.01 r_angle_other_deg 0.948 r_symmetry_hbond_refined 0.55 r_symmetry_vdw_other 0.329 r_metal_ion_refined 0.324 r_mcbond_other 0.235 r_nbd_refined 0.203 r_nbd_other 0.195 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.086 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing