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Crystal structure of the HePTP catalytic domain C270S mutant crystallized in ammonium acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZC0 PDB ENTRY 1ZC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.07 M AMMONIUM ACETATE, 0.07 M BIS-TRIS, 12% POLYETHYLENE GLYCOL 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.18 70.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.131 α = 90 b = 127.131 β = 90 c = 60.538 γ = 120
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 Si(111) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR 2006-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9795 NSLS X6A
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 2.72 50 99.2 0.122 6.6 4.2 15103 14980 1 1
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 2.72 2.82 98.4 0.601 4.1
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 (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 PDB ENTRY 1ZC0 2.72 20 14410 14314 752 99.33 0.16055 0.15709 0.1534 0.22681 0.2222 RANDOM 28.506
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] -0.25 -0.12 -0.25 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.231 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 17.817 r_scangle_it 10.128 r_scbond_it 7.5 r_dihedral_angle_1_deg 7.055 r_mcangle_it 4.555 r_mcbond_it 2.862 r_angle_refined_deg 2 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.231 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 17.817 r_scangle_it 10.128 r_scbond_it 7.5 r_dihedral_angle_1_deg 7.055 r_mcangle_it 4.555 r_mcbond_it 2.862 r_angle_refined_deg 2 r_nbtor_refined 0.329 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling