X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 323.0
Details 8% MPD, 100 mM Na acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 323K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.5 α = 90
b = 82.5 β = 90
c = 310.17 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97934, 0.97947, 0.94225 APS 19-ID

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 50 98.5 -- -- -- -- 128981 128981 0.0 0.0 --
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)
2.0 2.103 90.2 -- -- -- -- --

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
MAD 2.02 50.0 0.0 0.0 -- 128981 6829 99.1 -- 0.20999 0.20872 0.23442 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 2.02 2.08 7911 457 -- 0.21 0.24 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.58
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.702
r_scangle_it 2.789
r_mcangle_it 1.012
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 3.371
r_mcbond_it 0.534
r_angle_refined_deg 1.428
r_dihedral_angle_3_deg 17.007
r_chiral_restr 0.08
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2605
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12856
Nucleic Acid Atoms 0
Heterogen Atoms 323
Solvent Atoms 903

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
REFMAC refinement version: 5.0