X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop Streak Seeding Soaking
pH 6
Temperature 20.0
Details 1.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, soaking in 30 mM ATP, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.45 α = 90
b = 64.45 β = 90
c = 195.9 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-04-07
Diffraction Radiation
Monochromator Protocol
silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.936 ESRF ID29

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
2.3 19.76 99.4 -- 0.107 -- 6.9 21648 21648 0.0 -3.0 41.0
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)
2.3 2.42 100.0 -- 0.381 1.9 7.2 2977

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
OTHER 2.3 19.76 -- 0.0 21577 21577 1054 99.1 0.238 0.236 0.236 0.28 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 2.3 2.44 3345 165 3345 0.247 0.309 0.024 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.9
Anisotropic B[1][1] 6.08
Anisotropic B[1][2] 4.7
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.17
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 6.32
c_scbond_it 5.06
c_mcangle_it 5.31
c_mcbond_it 3.41
c_improper_angle_d 1.09
c_dihedral_angle_d 21.0
c_angle_deg 1.5
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) -0.02
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2905
Nucleic Acid Atoms 0
Heterogen Atoms 63
Solvent Atoms 205

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS 1.0 Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS version: 1.0 model building
SCALA data reduction
MOSFLM data collection