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Crystal Structure of MPK3 from Leishmania donovani, LdBPK_100540 in the presence of NVP-BBT594
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GCP ffas03 all atom model of 3gcp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1 M Citrate, 0.5 M Ammonium Sulfate, 1.0 M Lithium Sulfate, 1 mM NVP-BBT594, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.24 62.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.141 α = 90 b = 87.141 β = 90 c = 295.1 γ = 90
Symmetry Space Group I 41 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 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID .97918 APS 19-ID
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 2.71 49.18 99.8 0.062 24.4 10.2 16069 16037 100.02
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 2.71 2.84 99.1 0.015 1.5 10.2 2052
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 (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 ffas03 all atom model of 3gcp 2.71 48.87 16009 15989 803 99.87 0.2416 0.2403 0.2487 0.2664 0.2855 RANDOM 103.6868
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] -15.0933 -15.0933 30.1865
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.89 t_omega_torsion 1.73 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.89 t_omega_torsion 1.73 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2813 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction SBC-Collect data collection XSCALE data scaling BUSTER refinement