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Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 30% PEG 4000, 0.1M Na Citrate, 0.2M NH4 Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.54 α = 90 b = 74.521 β = 90 c = 79.006 γ = 90
Symmetry Space Group P 21 21 21
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 BEAMLINE OPTICS 2003-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 APS 14-BM-C
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 1.5 54.233 98.4 0.08 12.1 56178 56178 -1 -1
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) 1.5 1.55 99.7 0.743 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1QNP 1.5 20 -1 53236 53236 2853 98.5 0.18364 0.18364 0.18248 0.2451 0.20479 0.2504 RANDOM 18.865
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] 0.43 -1.22 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.423 r_scangle_it 2.571 r_scbond_it 1.606 r_angle_refined_deg 1.224 r_mcangle_it 1.084 r_angle_other_deg 0.781 r_mcbond_it 0.591 r_nbd_other 0.237 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.423 r_scangle_it 2.571 r_scbond_it 1.606 r_angle_refined_deg 1.224 r_mcangle_it 1.084 r_angle_other_deg 0.781 r_mcbond_it 0.591 r_nbd_other 0.237 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_other 0.222 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.103 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3143 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing