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METHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPEN CONFORMATION REPRESENTING SUBSTRATE-FREE STATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1REQ PDB ENTRY 1REQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 2MM COA, 1MM DTT, TRIS -HCL PH 7.5. RESERVOIR SOLUTION: 17.5% (W/V) PEG4000, 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION WERE MIXED AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.95 α = 90 b = 162.06 β = 108.75 c = 104.2 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 180 mm plate TOROIDAL MIRROR, SI MONOCHROMATOR 1995-07-26 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.5 20 99.8 0.092 6 4.8 113512 3.5 55
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 2.5 2.64 99.7 0.338 2.1 3.7
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-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 1REQ 2.5 20 113303 4538 99.6 0.259 0.2238 0.325 0.277 RANDOM 47
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 34.4 p_staggered_tor 19.8 p_planar_tor 5.9 p_scangle_it 5.102 p_mcangle_it 3.74 p_scbond_it 3.713 p_mcbond_it 2.424 p_multtor_nbd 0.17 p_chiral_restr 0.141 p_singtor_nbd 0.129
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 34.4 p_staggered_tor 19.8 p_planar_tor 5.9 p_scangle_it 5.102 p_mcangle_it 3.74 p_scbond_it 3.713 p_mcbond_it 2.424 p_multtor_nbd 0.17 p_chiral_restr 0.141 p_singtor_nbd 0.129 p_xyhbond_nbd 0.128 p_planar_d 0.046 p_angle_d 0.041 p_plane_restr 0.03 p_bond_d 0.012 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20360 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 244
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling