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Crystal Structure of subunit C (vma5p) of the yeast V-ATPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 PEG 3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.9 68.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.537 α = 90 b = 62.537 β = 90 c = 337.375 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 100 CCD ADSC QUANTUM 4 2004-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 20 99 0.072 0.072 39.67 5.9 69253 68620 2 -3 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 99.1 0.66 0.707 2.73 6 6709
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 1.75 20 69345 65150 3468 99.19 0.21096 0.21096 0.20973 0.2085 0.23442 0.2317 RANDOM 35.546
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 -0.11 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.697 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_4_deg 12.929 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.232 r_scbond_it 2.707 r_mcangle_it 1.725 r_angle_refined_deg 1.363 r_mcbond_it 1.006 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.697 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_4_deg 12.929 r_dihedral_angle_1_deg 5.668 r_scangle_it 4.232 r_scbond_it 2.707 r_mcangle_it 1.725 r_angle_refined_deg 1.363 r_mcbond_it 1.006 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.231 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2904 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing