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_mcangle_it 1.275
r_mcbond_other 0.776
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.484
r_angle_other_deg 0.775
r_dihedral_angle_1_deg 6.414
r_dihedral_angle_2_deg 30.396
r_dihedral_angle_3_deg 11.906
r_dihedral_angle_4_deg 18.301
r_chiral_restr 0.084
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 0.777
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

Computing
Computing Package Purpose
StructureStudio Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.2 molecular replacement
Xscale data reduction