X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details sitting drop, temperature 289K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.77 α = 77.88
b = 58.86 β = 77.8
c = 97.59 γ = 79.97
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2

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
2.4 39.93 97.7 0.066 -- -- 1.91 -- 47355 2.0 1.5 --
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)
2.4 2.49 97.5 0.521 -- 1.5 1.92 4721

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 2.4 39.922 -- 1.98 -- 47337 2407 97.7 -- 0.2001 0.1976 0.2446 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 2.4 2.449 -- 148 2717 0.3236 0.3693 -- 98.0
X Ray Diffraction 2.449 2.5022 -- 132 2591 0.3216 0.3953 -- 97.0
X Ray Diffraction 2.5022 2.5604 -- 157 2665 0.2969 0.3321 -- 98.0
X Ray Diffraction 2.5604 2.6244 -- 138 2597 0.2623 0.3584 -- 98.0
X Ray Diffraction 2.6244 2.6954 -- 128 2685 0.2707 0.3622 -- 98.0
X Ray Diffraction 2.6954 2.7747 -- 126 2643 0.2551 0.3349 -- 98.0
X Ray Diffraction 2.7747 2.8642 -- 138 2640 0.2632 0.3652 -- 98.0
X Ray Diffraction 2.8642 2.9666 -- 163 2628 0.2616 0.291 -- 98.0
X Ray Diffraction 2.9666 3.0853 -- 138 2694 0.2431 0.3337 -- 98.0
X Ray Diffraction 3.0853 3.2256 -- 148 2607 0.2312 0.3265 -- 99.0
X Ray Diffraction 3.2256 3.3956 -- 155 2621 0.2179 0.2792 -- 98.0
X Ray Diffraction 3.3956 3.6082 -- 138 2698 0.206 0.2583 -- 99.0
X Ray Diffraction 3.6082 3.8866 -- 145 2652 0.1691 0.2147 -- 98.0
X Ray Diffraction 3.8866 4.2773 -- 135 2652 0.1513 0.2122 -- 98.0
X Ray Diffraction 4.2773 4.8953 -- 132 2634 0.1488 0.185 -- 96.0
X Ray Diffraction 4.8953 6.1639 -- 141 2607 0.1699 0.1738 -- 97.0
X Ray Diffraction 6.1639 39.9276 -- 145 2599 0.1892 0.2153 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.2933
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.042
f_plane_restr 0.006
f_chiral_restr 0.048
f_angle_d 1.129
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7402
Nucleic Acid Atoms 1431
Heterogen Atoms 32
Solvent Atoms 238

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.9.1L data reduction
D*trek data collection