X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.4
Temperature 294.0
Details MPD, sodium acetate, calcium chloride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.46 α = 90
b = 87.93 β = 106.78
c = 124.39 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 1996-04-08
Diffraction Radiation
Monochromator Protocol
GERMANIUM CRYSTAL SET TO BRAGG REFLECTION (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX7.2 1.488 SRS PX7.2

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
2.8 30 98.0 0.05 0.05 -- 3.5 38321 38321 0.0 0.0 80.3
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)
2.8 2.82 99.7 0.61 0.61 1.92 3.5 982

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 30.0 0.0 0.0 36893 36893 1900 94.3 0.26 0.26 0.259 0.28 5% OF REFLECTIONS SELECTED IN THIN RESOLUTION SHELLS TO AVOID BIAS FROM NON-CRYSTALLOGRAPHIC SYMMETRY
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 2.98 5527 304 5527 0.365 0.39 0.022 90.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 75.8
Anisotropic B[1][1] -2.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 11.2
Anisotropic B[2][2] -1.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.1
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.97
c_dihedral_angle_d 26.1
c_angle_deg 1.398
c_bond_d 0.011
c_scangle_it 5.24
c_scbond_it 3.64
c_mcangle_it 4.76
c_mcbond_it 2.99
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10481
Nucleic Acid Atoms 0
Heterogen Atoms 145
Solvent Atoms 64

Software

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