X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details MPD, magnesium chloride, sodium cacodylate, spermine, sodium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.3 α = 90
b = 125.4 β = 90
c = 145.7 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 W16 wiggler 1999-03-24
Diffraction Radiation
Monochromator Protocol
single crystal, cylindrically bent SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 1.1 ALS 5.0.1

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
2.25 30 98.0 0.051 -- -- 4.8 64900 64900 -- -3.0 --
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)
2.25 2.33 99.3 0.578 57.8 2.4 4.4 6463

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 2.25 30.0 0.0 0.0 66170 60667 3017 91.7 -- -- 0.244 0.264 used the same Rfree reflection set as was used for 1gid which was then extended to include a random (10%) selection of the newly observed reflections.
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 2.25 2.39 -- 433 -- 0.5018 0.5092 -- 83.4
X Ray Diffraction 2.39 2.58 -- 525 -- 0.4233 0.4434 -- 87.4
X Ray Diffraction 2.58 2.83 -- 477 -- 0.3475 0.3723 -- 93.0
X Ray Diffraction 2.83 3.24 -- 551 -- 0.2618 0.2878 -- 97.1
X Ray Diffraction 3.24 4.09 -- 534 -- 0.2278 0.2582 -- 97.8
X Ray Diffraction 4.09 30.0 -- 497 -- 0.1932 0.2042 -- 90.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 75.4
Anisotropic B[1][1] 13.601
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -31.573
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.972
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.50534
c_improper_angle_d 2.16594
c_bond_d 0.010535
c_dihedral_angle_d 16.9863
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.45
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 6741
Heterogen Atoms 181
Solvent Atoms 126

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing