X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 39.66 mg/mL MymaA.00305.a.A1 PS00827 against PACT screen condition F10: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218672f10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.7 α = 90
b = 87.7 β = 90
c = 87.7 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2011-01-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT -- -- --

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
2.4 50 99.9 0.063 -- -- 7.1 9052 9040 -- -3.0 46.082
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)
2.4 2.46 100.0 0.519 -- 4.33 7.1 667

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 2.4 50.0 -- 0.0 -- 9002 471 99.45 -- 0.1821 0.1796 0.229 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 2.401 2.463 -- 39 624 0.206 0.283 -- 99.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.3734
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 32.43
r_chiral_restr 0.083
r_dihedral_angle_4_deg 15.943
r_scangle_it 3.251
r_bond_refined_d 0.014
r_gen_planes_refined 0.006
r_scbond_it 1.996
r_mcbond_it 0.622
r_mcangle_it 1.157
r_angle_refined_deg 1.323
r_dihedral_angle_1_deg 5.679
r_dihedral_angle_3_deg 13.999
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1443
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 65

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
StructureStudio data collection
XDS data reduction