X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 290.0
Details HAMPTON RESEARCH INDEX H12: 30% PEG 2000 MME, 150MM KBR, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K; 18 hour soak in reservoir solution containing 1mM actinonin

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.25 α = 80.87
b = 65.78 β = 76.82
c = 68.29 γ = 82.75
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ RIGAKU VARIMAX 2012-02-07
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 SSRL 7-1

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 99.6 0.077 0.077 -- 5.8 56808 56579 0.0 -3.0 22.89
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 1.95 98.0 0.49 0.49 2.02 2.5 4200

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 50.0 -- 0.0 56808 56577 2852 99.6 0.185 0.185 0.182 0.235 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 1.9 1.95 4114 198 3908 0.263 0.299 -- 97.93
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 18.66
Anisotropic B[1][1] -0.18
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.4
Anisotropic B[2][2] 0.7
Anisotropic B[2][3] -0.1
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.084
r_dihedral_angle_4_deg 13.148
r_dihedral_angle_3_deg 12.543
r_dihedral_angle_2_deg 33.807
r_dihedral_angle_1_deg 6.033
r_angle_other_deg 0.924
r_angle_refined_deg 1.603
r_bond_other_d 0.001
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5570
Nucleic Acid Atoms 0
Heterogen Atoms 117
Solvent Atoms 564

Software

Computing
Computing Package Purpose
JDIrector Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER_MR Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASER_MR model building
JDIrector data collection