X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.98 α = 90
b = 60.28 β = 93.43
c = 37.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2008-06-15
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
2.1 60.28 100.0 0.0816 0.0349 -- 15.45 8220 8216 0.0 0.0 38.6
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)
2.1 2.2 100.0 0.388 0.2114 4.49 11.86 1058

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 2.1 23.29 -- 0.0 8181 8181 803 99.78 0.215 0.215 0.209 0.278 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 2.1 2.154 585 60 521 0.303 0.365 -- 99.316
X Ray Diffraction 2.154 2.213 600 67 -- 0.247 0.35 -- 99.5
X Ray Diffraction 2.216 2.276 548 61 -- 0.244 0.327 -- 99.635
X Ray Diffraction 2.276 2.346 563 65 -- 0.243 0.354 -- 99.467
X Ray Diffraction 2.346 2.422 527 53 -- 0.249 0.384 -- 100.0
X Ray Diffraction 2.422 2.506 529 46 -- 0.249 0.338 -- 99.811
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.224
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.985
r_scbond_it 2.636
r_mcangle_it 1.683
r_mcbond_it 0.934
r_gen_planes_refined 0.008
r_chiral_restr 0.095
r_dihedral_angle_4_deg 14.772
r_dihedral_angle_3_deg 17.072
r_dihedral_angle_2_deg 33.39
r_dihedral_angle_1_deg 7.064
r_angle_refined_deg 1.216
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1034
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 45

Software

Computing
Computing Package Purpose
APEX Data Collection
SAINT Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0036 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 version: 5.5.0036 refinement
Phaser molecular replacement
SAINT collection/data indexing