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

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_scangle_it 4.78
x_scbond_it 3.74
x_mcangle_it 3.48
x_mcbond_it 2.48
x_torsion_impr_deg 0.69
x_torsion_deg 25.9
x_angle_deg 1.2
x_bond_d 0.005
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 2304
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 204

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, SHARP Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement