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Crystal structure of phzF from Pseudomonas fluorescens 2-79
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P9V pdb entry 1P9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 Reservoir solution: 0.20 M ammonium sulfate, 0.10 M sodium citrate pH 5.6 and 18% (w/v) PEG 4000. The protein concentration was 17 mg/ml, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.22 α = 90 b = 56.22 β = 90 c = 155.06 γ = 120
Symmetry Space Group P 32 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 105 IMAGE PLATE RIGAKU RAXIS IV++ MSC Blue Confocal Optics 2004-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.8 52 99.7 0.047 19.4 4.9 27247 27247
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) 1.8 1.86 96.9 0.175 4.7 2.89 2593
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 1P9V 1.8 20 25783 1361 99.86 0.18774 0.18597 0.1872 0.22209 0.2213 RANDOM 23.368
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] 0.29 0.14 0.29 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.259 r_scangle_it 5.185 r_scbond_it 3.222 r_angle_refined_deg 1.833 r_mcangle_it 1.794 r_mcbond_it 0.993 r_symmetry_hbond_refined 0.489 r_nbd_refined 0.202 r_chiral_restr 0.186 r_symmetry_vdw_refined 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.259 r_scangle_it 5.185 r_scbond_it 3.222 r_angle_refined_deg 1.833 r_mcangle_it 1.794 r_mcbond_it 0.993 r_symmetry_hbond_refined 0.489 r_nbd_refined 0.202 r_chiral_restr 0.186 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.156 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2120 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling RESOLVE phasing