X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 289.0
Details 30% PEG 3350, 0.1M Tris(hydroxymethyl)aminomethane hydrochloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.97 α = 90
b = 58.74 β = 90
c = 136.16 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2010-11-23
Diffraction Radiation
Monochromator Protocol
Si (111) horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13

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
1.55 19.45 94.5 0.069 -- -- 3.7 51271 51271 0.0 0.0 13.5
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)
1.55 1.63 95.9 0.498 -- 2.5 3.5 7498

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 1.55 19.36 -- 0.0 48582 48582 2610 94.05 0.20639 0.20639 0.20385 0.25371 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 1.55 1.59 -- 179 3377 0.247 0.333 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.129
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.255
r_sphericity_free 23.768
r_rigid_bond_restr 1.436
r_gen_planes_refined 0.003
r_chiral_restr 0.066
r_dihedral_angle_4_deg 16.193
r_dihedral_angle_3_deg 12.741
r_dihedral_angle_2_deg 28.488
r_dihedral_angle_1_deg 4.956
r_angle_refined_deg 0.967
r_bond_refined_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2138
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2722
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 412

Software

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