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human formylglycine generating enzyme, C336S mutant, bromide co-crystallization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.158 α = 90 b = 108.792 β = 90 c = 43.057 γ = 90
Symmetry Space Group P 21 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 MARRESEARCH 2006-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.63 50 97.7 0.075 15 3.5 35818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.69 78.2 0.396 3 3 2823
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2afy 1.64 27.2 33959 1726 99.04 0.15516 0.15338 0.19067 0.1885 RANDOM 12.435
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] 0.16 0.23 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.461 r_dihedral_angle_4_deg 15.797 r_dihedral_angle_3_deg 13.133 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.599 r_angle_other_deg 2.074 r_scbond_it 1.667 r_angle_refined_deg 1.31 r_mcangle_it 1.128 r_mcbond_it 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.461 r_dihedral_angle_4_deg 15.797 r_dihedral_angle_3_deg 13.133 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.599 r_angle_other_deg 2.074 r_scbond_it 1.667 r_angle_refined_deg 1.31 r_mcangle_it 1.128 r_mcbond_it 0.751 r_symmetry_vdw_refined 0.397 r_symmetry_vdw_other 0.347 r_nbd_other 0.23 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.201 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.156 r_metal_ion_refined 0.1 r_nbtor_other 0.096 r_mcbond_other 0.077 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling