X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.12 α = 90
b = 59.91 β = 95.03
c = 38.48 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
CCD DECTRIS PILATUS 6M -- 2012-02-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25

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
1.7 50 99.8 0.071 -- -- 6.1 15561 15561 0.0 0.0 30.7
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)
1.7 1.73 99.9 0.167 -- 10.3 5.5 783

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 1.7 38.33 -- 0.0 15543 15543 776 99.48 0.1646 0.1646 0.1628 0.1973 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 1.7 1.742 1076 57 1019 0.186 0.216 -- 94.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.1256
Anisotropic B[1][1] -1.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.71
Anisotropic B[2][2] -1.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.72
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.016
r_chiral_restr 0.139
r_dihedral_angle_4_deg 7.43
r_dihedral_angle_3_deg 14.442
r_dihedral_angle_2_deg 33.661
r_dihedral_angle_1_deg 6.413
r_angle_refined_deg 1.865
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1027
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 123

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement
SCALEPACK data reduction