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Endopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5C PDB ENTRY 1K5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.66 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.5 α = 72.39 b = 52.07 β = 69.5 c = 37.23 γ = 70.54
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MAR CCD 165 mm 2001-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.6 SPring-8 BL44B2
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 1.15 12.1 97.3 0.071 6.5 2.2 104270 104270 1 1 5.6
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 1.15 1.21 96.2 0.251 2.8 2.2 15075
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 1K5C 1.15 10 99036 104207 5171 92.6 0.1276 0.1257 0.1252 0.1635 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 11 2925.52
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.09 s_zero_chiral_vol 0.077 s_approx_iso_adps 0.072 s_similar_adp_cmpnt 0.039 s_from_restr_planes 0.0331 s_angle_d 0.03 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 55
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement SHELXL-97 refinement CCP4 data scaling