X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293The protein (concentrated to 15mg/mL in 20mM HEPES pH 7.5 and 150 mM NaCl) was crystallized at 293 K in 30% PEG2000 MME, 0.15M KBr with bromosporine using the sitting drop method.
Crystal Properties
Matthews coefficientSolvent content
2.3246.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.176α = 90
b = 77.176β = 90
c = 169.496γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97921APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.65098.90.0990.1020.02510.117.79764
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6498.50.6980.7180.1650.98418.7454

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5C8G2.650922051599.210.230.22750.2772RANDOM69.331
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]
2.151.082.15-6.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.776
r_dihedral_angle_3_deg12.92
r_dihedral_angle_4_deg10.654
r_dihedral_angle_1_deg5.069
r_mcangle_it1.73
r_angle_refined_deg1.136
r_angle_other_deg1.06
r_mcbond_it1.029
r_mcbond_other1.028
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.776
r_dihedral_angle_3_deg12.92
r_dihedral_angle_4_deg10.654
r_dihedral_angle_1_deg5.069
r_mcangle_it1.73
r_angle_refined_deg1.136
r_angle_other_deg1.06
r_mcbond_it1.029
r_mcbond_other1.028
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1935
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms58

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction