X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.35
Temperature 292.0
Details 25% PEG 4000, 0.1M sodium cacodylate,150 MM NACL, 50 mM IMIDAZOLE (PH=6.5), 10 MM MANGANESE CHLORIDE, 5 MM BETA-GLYCEROPHOSPHATE, 10mM mannose 6-phosphate, pH 6.35, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.16 α = 90
b = 84.75 β = 90
c = 96.05 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 128
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Bent conical Si-mirror (Rh coating) 2002-08-22
Diffraction Radiation
Monochromator Protocol
Bent Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 0.900 APS 14-ID-B

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
1.75 19.94 86.1 0.045 -- -- -- 51090 51090 0.0 0.0 15.7
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)
1.75 1.81 29.8 -- -- -- -- --

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
MIR 1.8 19.94 -- 1.0 46967 40876 2820 87.1 -- -- 0.235 0.283 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 1.8 1.88 2634 170 2464 0.35 0.382 0.029 45.6
X Ray Diffraction 1.88 1.98 4088 271 3817 0.33 0.375 0.023 70.4
X Ray Diffraction 1.98 2.1 5163 399 4764 0.287 0.347 0.017 88.8
X Ray Diffraction 2.1 2.27 5562 388 5174 0.261 0.311 0.016 95.3
X Ray Diffraction 2.27 2.49 5693 389 5304 0.246 0.311 0.016 97.4
X Ray Diffraction 2.49 2.86 5776 388 5388 0.244 0.315 0.016 98.7
X Ray Diffraction 2.86 3.59 5898 395 5503 0.222 0.268 0.013 99.4
X Ray Diffraction 3.59 19.94 6062 420 5642 0.206 0.237 0.012 98.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.19
Anisotropic B[1][1] 0.615
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.453
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.068
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.416
x_mcangle_it 2.666
x_scbond_it 2.372
x_mcbond_it 1.62
x_torsion_impr_deg 0.72
x_torsion_deg 26.8
x_angle_deg 1.4
x_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3303
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 365

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
SOLVE/RESOLVE model building
SCALEPACK data reduction
DENZO data collection