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Crystal structure of the flavodiiron protein from Giardia intestinalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCF PDB ENTRY 1YCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 16% PEG 3350, 0.2 M potassium nitrate,0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.967 α = 90 b = 115.059 β = 90 c = 67.732 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 ADSC QUANTUM 315 toroidal mirror 2006-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0 ESRF ID29
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 1.9 80 98.3 0.087 9.4 7.3 70973 69601 0.015 17.7
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) 1.9 1.97 92.3 0.43
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 1YCF 1.9 50 65166 3469 98.51 0.16664 0.16461 0.1664 0.20409 0.2023 RANDOM 17.233
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] -0.67 -0.39 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.092 r_scangle_it 3.148 r_scbond_it 2.11 r_angle_refined_deg 1.393 r_mcangle_it 1.218 r_mcbond_it 0.811 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.092 r_scangle_it 3.148 r_scbond_it 2.11 r_angle_refined_deg 1.393 r_mcangle_it 1.218 r_mcbond_it 0.811 r_nbtor_refined 0.305 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.101 r_metal_ion_refined 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6428 Nucleic Acid Atoms Solvent Atoms 776 Heterogen Atoms 88
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling