X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 303.15
Details CRYSTALLIZED FROM 1.60-1.90 M (NH4)2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION OF 2.20 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M BIS-TRIS-HCL PH 6.0. SOAK CONDITIONS: CRYSTALS WERE SOAKED IN STABILISATION SOLUTION CONTAINING 0.002 M LUTETIUM CHLORIDE HEXAHYDRATE. CRYOPROTECTION CONDITIONS: AFTER ADDITION OF 20% GLYCEROL (W/V) TO THE SOAK SOLUTION, CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN., VAPOR DIFFUSION, SITTING DROP, temperature 303.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.7 α = 90
b = 69.7 β = 90
c = 84.1 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-08-01
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0302, 1.3366, 1.3369, 0.9968, 1.3359 ELETTRA 5.2R

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
2.7 22.5 98.5 0.076 -- -- 4.2 12371 12371 0.0 0.0 100.3
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)
2.7 2.8 100.0 0.593 -- 2.1 4.1 --

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
MAD 2.7 22.5 0.0 0.0 12560 10539 909 83.9 0.271 0.244 0.23 0.245 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 2.7 2.82 -- 86 858 0.531 0.531 0.057 60.0
X Ray Diffraction 2.82 2.97 -- 106 1022 0.437 0.437 0.042 72.3
X Ray Diffraction 2.97 3.16 -- 119 1150 0.363 0.364 0.033 80.4
X Ray Diffraction 3.16 3.4 -- 117 1292 0.312 0.312 0.029 89.7
X Ray Diffraction 3.4 3.74 -- 108 1287 0.251 0.251 0.024 89.9
X Ray Diffraction 3.74 4.29 -- 132 1295 0.229 0.229 0.02 91.1
X Ray Diffraction 4.29 5.4 -- 114 1417 0.176 0.176 0.016 97.0
X Ray Diffraction 5.4 60.36 -- 125 1300 0.155 0.154 0.014 90.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 80.6
Anisotropic B[1][1] 26.51
Anisotropic B[1][2] 21.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 26.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -53.03
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.24
c_dihedral_angle_d 15.6
c_bond_d 0.006
c_angle_deg 1.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.5
Luzzati Sigma A (Observed) 0.92
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.9
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 970
Heterogen Atoms 12
Solvent Atoms 6

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS model building
CNS refinement