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Structure of CBM35 from Paenibacillus barcinonensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VZP PDB ENTRY 2VZP, 4QAW (CBM35) experimental model PDB 4QAW PDB ENTRY 2VZP, 4QAW (CBM35)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 20% PEG 6000, 0.2M Calcium chloride, 0.1M MES, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.4 α = 90 b = 47.45 β = 90 c = 103.02 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 120 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2014-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54179
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 2.18 51.51 97.5 0.068 0.02 25.7 11.9 123458 10371 1 1 12.94
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 2.18 2.3 83.8 0.169 0.051 12.9 11.6 1270
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VZP, 4QAW (CBM35) 2.19 51.51 1 1 123458 10371 494 98.6 0.21209 0.20923 0.26885 0.2498 RANDOM 17.006
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] 2.21 -0.76 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.247 r_dihedral_angle_4_deg 26.088 r_dihedral_angle_3_deg 13.499 r_dihedral_angle_1_deg 6.792 r_long_range_B_refined 2.618 r_long_range_B_other 2.509 r_scangle_other 1.534 r_mcangle_other 1.309 r_mcangle_it 1.306 r_angle_refined_deg 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.247 r_dihedral_angle_4_deg 26.088 r_dihedral_angle_3_deg 13.499 r_dihedral_angle_1_deg 6.792 r_long_range_B_refined 2.618 r_long_range_B_other 2.509 r_scangle_other 1.534 r_mcangle_other 1.309 r_mcangle_it 1.306 r_angle_refined_deg 1.29 r_scbond_other 0.99 r_scbond_it 0.989 r_mcbond_it 0.801 r_mcbond_other 0.786 r_angle_other_deg 0.707 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 974 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling