X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 292.0
Details PEG4000, TRIS-HCL, ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.16 α = 90
b = 51.19 β = 90
c = 123.47 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 ADSC QUANTUM 4 MIRROR 2000-06-03
Diffraction Radiation
Monochromator Protocol
SILICON 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.98789, 1.01000, 1.03473, 1.04008 NSLS X9B

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
2.15 40 99.5 0.038 -- -- 4.161 16542 16542 0.0 0.0 48.0
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)
2.15 2.23 99.9 0.37 -- 3.258 4.025 1621

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
MIR 2.15 30.0 2.0 4.0 15686 13894 -- 94.8 -- 0.2075 0.2119 0.275 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 2.15 2.25 1712 -- -- 0.292 -- -- --
X Ray Diffraction 2.25 2.35 1439 -- -- 0.278 -- -- --
X Ray Diffraction 2.35 2.48 1640 -- -- 0.257 -- -- --
X Ray Diffraction 2.48 2.66 1520 -- -- 0.217 -- -- --
X Ray Diffraction 2.66 2.86 1619 -- -- 0.2 -- -- --
X Ray Diffraction 2.86 3.11 1488 -- -- 0.191 -- -- --
X Ray Diffraction 3.11 3.5 1618 -- -- 0.197 -- -- --
X Ray Diffraction 3.5 4.13 1559 -- -- 0.18 -- -- --
X Ray Diffraction 4.13 6.58 1529 -- -- 0.188 -- -- --
X Ray Diffraction 6.58 30.0 563 -- -- 0.288 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 54.404
RMS Deviations
Key Refinement Restraint Deviation
s_from_restr_planes 0.02
s_similar_adp_cmpnt 0.083
s_approx_iso_adps 0.0
s_rigid_bond_adp_cmpnt 0.0
s_anti_bump_dis_restr 0.019
s_zero_chiral_vol 0.041
s_similar_dist 0.0
s_bond_d 0.005
s_angle_d 0.018
s_non_zero_chiral_vol 0.051
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.263
Luzzati Resolution Cutoff (Low) 5.0
Number Disordered Residues 0.0
Occupancy Sum Hydrogen 0.0
Occupancy Sum Non Hydrogen 2696.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2444
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 252

Software

Software
Software Name Purpose
SHARP phasing
SHELXL-97 refinement
DENZO data reduction
SCALEPACK data scaling