X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 34% MPD, 25 mM potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.37 α = 90
b = 48.37 β = 90
c = 63.45 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Meridianally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification 2010-07-29
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- 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
1.9 50 99.7 0.073 -- -- 13.5 11646 11646 0.0 0.0 34.3
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)
1.9 1.93 99.3 0.283 -- -- 13.1 581

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 1.9 48.37 -- 0.0 11629 11629 555 99.7 0.1669 0.1669 0.1648 0.21 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 1.896 1.945 -- 52 805 0.181 0.249 -- 99.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.6141
Anisotropic B[1][1] 0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.19
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.445
r_scbond_it 3.606
r_mcangle_it 2.06
r_mcbond_it 1.382
r_gen_planes_refined 0.013
r_chiral_restr 0.159
r_dihedral_angle_4_deg 7.22
r_dihedral_angle_3_deg 15.921
r_dihedral_angle_2_deg 33.06
r_dihedral_angle_1_deg 6.103
r_angle_refined_deg 1.704
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1029
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 96

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
HKL data reduction