X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details sodium dihydrogen phosphate, potassium dihydrogen phosphate, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 231.61 α = 90
b = 231.61 β = 90
c = 88.59 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 27-pole hybrid wiggler and vertical focusing mirror 2001-02-28
Diffraction Radiation
Monochromator Protocol
double Si crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.9792 NSLS X25

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 20 98.3 0.082 0.082 -- 6.8 202265 198856 1.0 1.0 46.0
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)
2.4 2.49 92.3 0.409 0.409 2.5 -- 18706

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
Single anomalous scattering 2.42 20.0 0.0 0.0 192349 192349 18573 95.0 0.217 0.217 0.215 0.257 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 2.42 2.44 2983 259 -- 0.305 0.312 -- --
X Ray Diffraction 8.67 20.0 4055 368 -- 0.172 0.209 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Anisotropic B[1][1] 1.528
Anisotropic B[1][2] -5.718
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.528
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.055
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.025
c_scbond_it 3.162
c_mcangle_it 2.272
c_mcbond_it 1.348
c_angle_deg 1.319
c_bond_d 0.0066
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15000
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 779

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE, MLPHARE, DM Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SnB/Mlphare/DM model building