X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, crystal tracking ID 238414h7, unique puck ID gpy2-6, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.43 α = 90
b = 81.91 β = 96.51
c = 95.4 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ VariMax 2012-11-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
1.7 50 97.9 0.045 -- -- 4.6 93194 91223 -- -3.0 23.913
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.74 90.2 0.29 -- 3.22 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.7 45.74 -- 0.0 -- 91201 4566 97.89 -- 0.1747 0.1733 0.2015 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.744 -- 328 5886 0.219 0.255 -- 90.24
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.5464
Anisotropic B[1][1] -0.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.67
Anisotropic B[2][2] 0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.44
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_angle_refined_deg 1.484
r_mcbond_other 0.776
r_bond_other_d 0.001
r_angle_other_deg 0.775
r_mcbond_it 0.777
r_mcangle_it 1.275
r_dihedral_angle_2_deg 30.396
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 6.414
r_chiral_restr 0.084
r_dihedral_angle_3_deg 11.906
r_dihedral_angle_4_deg 18.301
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5570
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 697

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.2
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
StructureStudio data collection
XDS data reduction