5YSM

Crystal Structure Analysis of Rif16


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5277Magnesium chloride hexahydrate, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0439.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.105α = 90
b = 70.335β = 94.43
c = 81.019γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2017-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.976SSRFBL19U1

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
11.85094.10.0670.0730.02896.333798
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)
11.81.8390.60.4750.5190.2060.8956

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.940.4228027145994.740.18570.18310.2339RANDOM22.621
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]
-0.080.22-0.180.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.889
r_dihedral_angle_4_deg20.643
r_dihedral_angle_3_deg15.757
r_dihedral_angle_1_deg6.268
r_angle_refined_deg1.95
r_angle_other_deg0.945
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.889
r_dihedral_angle_4_deg20.643
r_dihedral_angle_3_deg15.757
r_dihedral_angle_1_deg6.268
r_angle_refined_deg1.95
r_angle_other_deg0.945
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.007
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2794
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms43

Software

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