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peptide deformylase (Ni-form) with hydrosulfide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W3T PDB ENTRY 2W3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 293 25% PEG 4000, 200 MM NAOAC PH 4.6, 293 K, INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.206 α = 90 b = 63.222 β = 144.28 c = 118.175 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 92 OSMIC MULTILAYER 2010-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.6 20 99.5 0.22 3.1 2.6 18933 -3 62.8
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 2.6 2.74 99.5 0.52 1.7 2.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2W3T 2.6 69 17955 975 99.33 0.2108 0.20616 0.2121 0.29781 0.303 RANDOM 65.594
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] -2.41 -1.02 0.81 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.051 r_dihedral_angle_4_deg 19.057 r_dihedral_angle_3_deg 18.914 r_dihedral_angle_1_deg 6.496 r_angle_refined_deg 1.441 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.051 r_dihedral_angle_4_deg 19.057 r_dihedral_angle_3_deg 18.914 r_dihedral_angle_1_deg 6.496 r_angle_refined_deg 1.441 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3932 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction SCALA data scaling PHASER phasing