X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 50mM imidazole pH 7.5, 200-400mM CaCl, 20% PEG 1k, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.75 α = 90
b = 60.62 β = 103.1
c = 58.4 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-06-25
Diffraction Radiation
Monochromator Protocol
Silicon (1 1 1) channel-cut, silicon toroidal mirror coated with Rhodium SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.072250 ESRF ID23-1

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
1.3 41.49 98.2 0.08 0.08 -- 2.8 65111 65111 -- -- --
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)
1.3 1.37 89.1 0.635 0.635 1.2 2.1 8579

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 1.3 41.487 -- 0.0 -- 64982 3294 100.0 -- 0.1324 0.1302 0.1736 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 1.3 1.334 -- 217 3826 0.273 0.269 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.7329
Anisotropic B[1][1] -0.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.22
Anisotropic B[2][2] 0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.301
r_bond_refined_d 0.01
r_angle_refined_deg 1.465
r_dihedral_angle_1_deg 5.567
r_dihedral_angle_2_deg 31.981
r_dihedral_angle_3_deg 10.438
r_dihedral_angle_4_deg 16.419
r_chiral_restr 0.091
r_gen_planes_refined 0.007
r_mcbond_it 1.299
r_mcangle_it 2.055
r_scbond_it 2.695
r_scangle_it 3.724
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2451
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 490

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA 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
SCALA version: 3.2.25 data reduction
Mosflm data collection