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Crystal structure of the Grp1 PH domain in complex with Arf6-GTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 291 50 mM Tris, 20% PEG 4000, 0.2 M sodium citrate. Microseeding and TCEP were needed for large crystal growth, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.85 56.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.595 α = 90 b = 56.595 β = 90 c = 274.371 γ = 90
Symmetry Space Group P 43 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 298 CCD ADSC QUANTUM 315 2010-12-03 M SINGLE WAVELENGTH 2 1 77
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 1.85 20 98.9 42545 41858 -3
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 1.85 1.86 98.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MOLECULAR REPLACEMENT THROUGHOUT 1.85 20 -3 42890 38245 2039 98.93 0.20185 0.20012 0.2001 0.23505 0.2374 RANDOM 32.841
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] 0.38 0.38 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.827 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 5.394 r_scangle_it 2.095 r_scbond_it 1.239 r_angle_refined_deg 1.142 r_mcangle_it 0.981 r_mcbond_it 0.519 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.827 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 5.394 r_scangle_it 2.095 r_scbond_it 1.239 r_angle_refined_deg 1.142 r_mcangle_it 0.981 r_mcbond_it 0.519 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2501 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 99
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling