☰ Navigation Tabs
meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant hexagonal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4X PDB ENTRY 1C4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.8 278 PEG4000, ammonium acetate, sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.797 α = 90 b = 98.797 β = 90 c = 149.34 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 100 DIFFRACTOMETER WEISSENBERG 1999-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B
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 2.8 50 98.7 0.095 0.095 13.5 6.1 21101 21088 17.8
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) 2.8 2.9 97.1 0.299 0.299 3.2 3.7 2041
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1C4X 2.8 49.78 21088 21088 1064 98.7 0.1988 0.1988 0.196 0.1979 0.251 0.1864 RANDOM 32.1
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] 5.93 7.15 5.93 -11.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 7.09 c_scbond_it 4.95 c_mcangle_it 4.73 c_mcbond_it 3.09 c_angle_deg 1.3 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 7.09 c_scbond_it 4.95 c_mcangle_it 4.73 c_mcbond_it 3.09 c_angle_deg 1.3 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4319 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 4
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling