X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 293.0
Details 10% MPD, 7% PEG 4000, 0.1M sodium citrate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.15 α = 90
b = 81.28 β = 90
c = 81.1 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-10-07
CCD ADSC QUANTUM 4 -- 2006-10-07
CCD ADSC QUANTUM 4 -- 2006-10-07
Diffraction Radiation
Monochromator Protocol
liquid nitrogen cooled channel-cut silicon monochromator SINGLE WAVELENGTH
liquid nitrogen cooled channel-cut silicon monochromator MAD
liquid nitrogen cooled channel-cut silicon monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID29 0.9791, 0.9792, 0.9756 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29

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
2.53 57.41 94.9 0.083 -- -- 4.6 15899 15899 0.0 0.0 59.298
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)
2.53 2.73 96.5 0.386 -- 2.9 4.6 2323

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
MAD 2.53 57.41 0.0 0.0 14986 14986 860 87.61 0.19891 0.19891 0.19587 0.2522 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 2.528 2.594 71 7 71 0.229 0.238 -- 5.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.786
Anisotropic B[1][1] 8.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.98
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_chiral_restr 0.114
r_dihedral_angle_4_deg 21.222
r_dihedral_angle_3_deg 21.409
r_dihedral_angle_2_deg 42.621
r_dihedral_angle_1_deg 6.556
r_angle_refined_deg 1.741
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3331
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 62

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.7.0024 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0024 refinement
SHARP model building
DNA data collection