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Crystal structure of LmNADK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I29 PDB ENTRY 2i29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.428 α = 90 b = 76.361 β = 90 c = 119.202 γ = 90
Symmetry Space Group I 2 2 2
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 315 2006-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 ESRF ID14-2
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 1.9 32.14 99 0.071 20.9 6.5 22583 21902 23.5
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 1.9 2 94 0.399 4.1 5.2
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 PDB ENTRY 2i29 1.9 32.14 22583 21902 681 98.85 0.206 0.206 0.205 0.2048 0.243 0.2382 RANDOM 24.318
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] 0.62 1.41 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 11.502 r_dihedral_angle_4_deg 10.04 r_angle_refined_deg 1.403 r_scangle_it 1.227 r_scbond_it 0.891 r_mcangle_it 0.663 r_mcbond_it 0.424 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 11.502 r_dihedral_angle_4_deg 10.04 r_angle_refined_deg 1.403 r_scangle_it 1.227 r_scbond_it 0.891 r_mcangle_it 0.663 r_mcbond_it 0.424 r_nbtor_refined 0.307 r_xyhbond_nbd_refined 0.303 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.143 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.113 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2051 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing