X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 290.0
Details 25% PEG8000, 5 mM MgCl2, 400 mM NaCl, Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.87 α = 84.13
b = 39.6 β = 72.09
c = 58.56 γ = 70.2
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE FUJI Double crystal monochromator with sagittally focussed second crystal. Two spherical mirrors. 1997-04-05
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator with sagittally focussed second crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.92016 NSLS X4A

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
2.7 18.62 97.0 0.09 -- -- 3.1 7671 7671 0.0 0.0 58.3
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)
2.7 2.8 92.7 0.44 -- 2.1 3.1 7691

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
MOLECULAR REPLACEMENT 2.8 18.6 0.0 0.0 6854 6854 732 96.9 0.2599 0.2599 0.2599 0.3103 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 2.8 2.9 -- 83 -- 0.5517 0.5721 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 60.81
Anisotropic B[1][1] -39.691
Anisotropic B[1][2] -1.626
Anisotropic B[1][3] -2.807
Anisotropic B[2][2] 10.855
Anisotropic B[2][3] -10.126
Anisotropic B[3][3] 28.836
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.8505
c_dihedral_angle_d 23.271
c_angle_deg 3.8266
c_bond_d 0.0165
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.52
Luzzati Sigma A (Observed) 1.06
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.56
Luzzati Sigma A (R-Free Set) 1.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1160
Nucleic Acid Atoms 814
Heterogen Atoms 4
Solvent Atoms 9

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection