X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 4.0
Details 0.1 M NaHEPES, 40% MPD, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 192.96 α = 90
b = 232.13 β = 90
c = 296.77 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH SSRL/9-1 2000-02-15
Diffraction Radiation
Monochromator Protocol
SSRL/9-1 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1

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
3.2 50 89.1 0.112 0.112 -- 2.7 -- 189495 -- 0.0 --
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)
3.2 3.26 62.9 0.331 0.331 1.9 2.5 --

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 3.2 50.0 -- 0.0 -- 189495 1028 86.6 -- 0.255 0.255 0.325 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 3.2 3.35 -- 65 13432 0.376 0.404 0.05 49.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 83.0
Anisotropic B[1][1] -1.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.5
x_bond_d 0.013
x_angle_deg 1.77
x_dihedral_angle_d 23.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.5
Luzzati Sigma A (Observed) 0.62
Luzzati ESD (R-Free Set) 0.65
Luzzati Sigma A (R-Free Set) 0.69
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 70608
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, CCP4, DM, RAVE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
RAVE model building
DM model building
CCP4 model building
AMORE model building