X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 277.0
Details 6% PEG 3350, 1M NaCl, 2 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.22 α = 90
b = 240.97 β = 90
c = 212.08 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2012-04-12
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
2.4 19.99 94.4 -- 0.106 -- 5.0 -- 29079 -- 0.0 55.3
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)
2.4 2.44 1.0 -- 0.39 2.3 2.8 --

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 2.4 19.99 -- 0.0 30646 29079 1567 49.7 -- 0.179 0.175 0.238 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 2.4 2.47 -- 2 66 0.27 0.406 -- 1.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 102.99
Anisotropic B[1][1] -0.97
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.84
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.096
r_dihedral_angle_1_deg 5.803
r_angle_refined_deg 1.066
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 30.435
r_mcbond_it 1.81
r_dihedral_angle_3_deg 14.391
r_chiral_restr 0.055
r_bond_refined_d 0.006
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_mcbond_other 1.808
r_dihedral_angle_4_deg 14.224
r_angle_other_deg 0.668
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 24.9
Luzzati ESD (R-Free Set) 39.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8220
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 131

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.7.0032
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data reduction
HKL-2000 data scaling