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Crystal structure of atp12p from paracoccus denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 278 30% PEG4000, 50 MM MGCL2, 100 MM TRIS VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.553 α = 90 b = 55.749 β = 90 c = 96.616 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 50 99.8 0.062 25.41 14.49 127208 127208
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 1.06 99.9 0.745 3.97 14.34
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 2P4X 1 50 127208 6370 99.8 0.1187 0.118 0.1309 0.1425 RANDOM 16.3
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 58 1806 2340.1
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.154 s_approx_iso_adps 0.108 s_zero_chiral_vol 0.089 s_similar_adp_cmpnt 0.033 s_angle_d 0.032 s_from_restr_planes 0.0262 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1833 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 8
Software Software Software Name Purpose MOLREP phasing SHELXL-97 refinement XDS data reduction XDS data scaling