X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop Macroseeding
pH 4.6
Temperature 277.0
Details 30% MPD, 0.1 M sodium acetate, 20 mM CaCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, MACROSEEDING, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.2 α = 90
b = 46.5 β = 90
c = 136.5 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2001-12-13
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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 43 92.7 -- 0.071 -- 9.0 35306 32726 1.0 1.0 26.2
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 2.55 61.5 -- 0.477 -- -- 3550

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 2.4 43.22 -- 0.0 35384 29457 1102 83.2 0.247 0.224 0.224 0.248 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 2.4 2.55 3494 56 3494 0.388 0.428 0.057 61.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 46.0
Anisotropic B[1][1] -25.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 36.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.76
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.53
c_scbond_it 1.77
c_mcangle_it 2.2
c_mcbond_it 1.31
c_improper_angle_d 0.97
c_dihedral_angle_d 26.4
c_angle_deg 1.4
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4199
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 229

Software

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