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 -- -- 7.9 741

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 -- -- 15360 14519 769 98.32 0.23873 0.23873 0.23741 0.26214 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 0.435 0.567 -- 89.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.39
Anisotropic B[1][1] -7.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.33
Anisotropic B[2][2] 0.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.73
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.009
r_angle_refined_deg 1.38
r_dihedral_angle_4_deg 14.646
r_dihedral_angle_2_deg 31.582
r_gen_planes_other 0.001
r_bond_refined_d 0.01
r_angle_other_deg 1.534
r_dihedral_angle_3_deg 14.752
r_chiral_restr 0.103
r_bond_other_d 0.003
r_dihedral_angle_1_deg 5.364
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

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
REFMAC refinement version: 5.7.0029
DENZO data reduction
SCALEPACK data scaling