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Structure of the N-terminal domain of XpsE (crystal form P43212)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 magnesium acetate, sodium cacodylate pH 6.5, PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.914 α = 90 b = 55.914 β = 90 c = 104.813 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 2004-02-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9537, 0.97990, 0.97980 SPring-8 BL12B2
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 28 99.4 0.045 12460 2 2
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 2.07 100 0.09 1161
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 MAD THROUGHOUT 2 28 12460 11783 570 99.55 0.192 0.192 0.189 0.2038 0.252 0.266 RANDOM 21.385
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] 0.28 0.28 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.273 r_scangle_it 5.55 r_scbond_it 3.657 r_mcangle_it 2.507 r_angle_refined_deg 2.175 r_mcbond_it 1.428 r_angle_other_deg 1.035 r_symmetry_vdw_refined 0.379 r_symmetry_vdw_other 0.342 r_nbd_refined 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.273 r_scangle_it 5.55 r_scbond_it 3.657 r_mcangle_it 2.507 r_angle_refined_deg 2.175 r_mcbond_it 1.428 r_angle_other_deg 1.035 r_symmetry_vdw_refined 0.379 r_symmetry_vdw_other 0.342 r_nbd_refined 0.266 r_nbd_other 0.264 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.112 r_nbtor_other 0.091 r_bond_refined_d 0.022 r_gen_planes_other 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1136 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling SHARP phasing