X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 310.0
Details Sodium phosphate, potassium phosphate, 1,4-butanediol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55 α = 90
b = 55 β = 90
c = 176.2 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate focusing mirrors 2000-03-28
CCD ADSC QUANTUM 4 -- 2000-04-05
Diffraction Radiation
Monochromator Protocol
Osmic Mirror SINGLE WAVELENGTH
Si 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54180 -- --
SYNCHROTRON SSRL BEAMLINE BL1-5 0.97943, 0.980035, 0.925256, 1.06883 SSRL BL1-5

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
1.76 20 99.9 0.056 -- -- 8.7 29261 26431 0.0 -3.0 20.7
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)
1.76 1.81 99.5 0.757 -- 2.6 6.3 --

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 1.83 20.0 0.0 0.0 26457 26447 1306 100.0 0.193 0.193 0.191 0.214 Random 5% of data
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 1.83 1.91 3260 145 3117 0.247 0.262 0.022 99.8
X Ray Diffraction 1.91 2.01 3296 140 3156 0.212 0.211 0.018 99.8
X Ray Diffraction 2.01 2.14 3319 169 3150 0.206 0.207 0.016 99.8
X Ray Diffraction 2.14 2.3 3320 178 3142 0.204 0.206 0.015 99.8
X Ray Diffraction 2.3 2.54 3281 148 3133 0.194 0.195 0.016 99.9
X Ray Diffraction 2.54 2.9 3330 173 3157 0.189 0.19 0.014 100.0
X Ray Diffraction 2.9 3.65 3317 193 3124 0.185 0.188 0.014 100.0
X Ray Diffraction 3.65 19.99 3324 160 3164 0.178 0.177 0.014 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.05
Anisotropic B[1][1] 2.93
Anisotropic B[1][2] 1.98
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.85
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_deg 25.9
x_torsion_impr_deg 0.69
x_bond_d 0.005
x_mcangle_it 3.48
x_angle_deg 1.2
x_scangle_it 4.78
x_scbond_it 3.74
x_mcbond_it 2.48
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2262
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 204

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
SHARP phasing