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Crystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FMN and ATP analog AMPCPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M Sodium acetate, pH 4.6, 8% (w/v) PEG 4000, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.07 40.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.831 α = 90 b = 81.753 β = 129.67 c = 136.698 γ = 90
Symmetry Space Group C 1 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 113 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2007-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 50 96.4 0.088 11.517 2.5 123738 123738 19.4
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) 1.95 2.02 97.1 0.447 2.094 2.5 12367
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 3FWK 1.95 35.07 123713 123713 6202 96.28 0.17845 0.178 0.175 0.1755 0.236 0.2362 RANDOM 19.286
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] 0.19 0.32 -0.16 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_4_deg 13.015 r_dihedral_angle_1_deg 6.105 r_mcangle_it 1.963 r_scangle_it 1.835 r_angle_refined_deg 1.432 r_mcbond_it 1.274 r_scbond_it 1.24 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.466 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_4_deg 13.015 r_dihedral_angle_1_deg 6.105 r_mcangle_it 1.963 r_scangle_it 1.835 r_angle_refined_deg 1.432 r_mcbond_it 1.274 r_scbond_it 1.24 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.094 r_metal_ion_refined 0.063 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14700 Nucleic Acid Atoms Solvent Atoms 1790 Heterogen Atoms 397
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing