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_rigid_bond_restr 1.436
r_dihedral_angle_3_deg 12.741
r_chiral_restr 0.066
r_bond_refined_d 0.005
r_dihedral_angle_2_deg 28.488
r_sphericity_free 23.768
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 4.956
r_sphericity_bonded 6.255
r_angle_refined_deg 0.967
r_dihedral_angle_4_deg 16.193
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

Software
Software Name Purpose
DNA data collection
PHASER phasing
REFMAC refinement version: 5.6.0117
XDS data reduction
SCALA data scaling