X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 0.01M Zinc chloride, 0.1M MES, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.67 α = 90
b = 40.98 β = 97.21
c = 52.04 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2011-10-07
Diffraction Radiation
Monochromator Protocol
OSMIC VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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 61.84 99.9 0.086 -- -- 8.0 15360 15360 0.0 0.0 --
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 2.14 100.0 0.898 -- -- 7.9 768

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 15.0 -- 0.0 -- 15288 769 98.33 -- 0.2253 0.2236 0.2558 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 2.098 2.153 -- 60 970 0.428 0.538 -- 89.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.0382
Anisotropic B[1][1] -3.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.4
Anisotropic B[2][2] 1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.34
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.277
r_scbond_it 3.015
r_mcangle_it 1.91
r_mcbond_other 0.264
r_bond_refined_d 0.006
r_bond_other_d 0.001
r_angle_refined_deg 1.183
r_angle_other_deg 0.91
r_dihedral_angle_1_deg 4.242
r_dihedral_angle_2_deg 28.896
r_dihedral_angle_3_deg 14.019
r_dihedral_angle_4_deg 10.504
r_chiral_restr 0.049
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_mcbond_it 1.042
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 909
Nucleic Acid Atoms 814
Heterogen Atoms 9
Solvent Atoms 57

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK 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
SCALEPACK data reduction
DENZO data collection