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Crystal structure of the phytase from D. castellii at 2.3 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.02M CaCl2
15% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.47 64.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.655 α = 90 b = 121.655 β = 90 c = 332.245 γ = 120
Symmetry Space Group P 65 2 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 2005-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.29 65.541 95.2 0.11 0.11 5 5.1 62779 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.42 83 84.3 0.219 0.219 3.1 2.8
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 (All) 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 1QFX 2.29 65.23 62778 3186 94.44 0.157 0.154 0.1563 0.21 0.2109 RANDOM 26.449
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] 0.07 0.04 0.07 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.153 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 13.537 r_sphericity_free 6.595 r_dihedral_angle_1_deg 6.258 r_scangle_it 3.919 r_scbond_it 2.987 r_sphericity_bonded 2.661 r_rigid_bond_restr 2.551 r_mcangle_it 1.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.153 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 13.537 r_sphericity_free 6.595 r_dihedral_angle_1_deg 6.258 r_scangle_it 3.919 r_scbond_it 2.987 r_sphericity_bonded 2.661 r_rigid_bond_restr 2.551 r_mcangle_it 1.754 r_angle_refined_deg 1.512 r_mcbond_it 1.04 r_nbtor_refined 0.32 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_refined 0.209 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7192 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 70
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling PHASER phasing