X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG 4000, Hepes, Sodium Acetate, NADP+, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.95 α = 90
b = 115.53 β = 90
c = 116.95 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 mirrors 1999-09-19
Diffraction Radiation
Monochromator Protocol
bent conical Si-mirror (Rh coating) + bent cylindrical Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0000 APS 14-BM-C

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
2.6 30 82.3 0.037 0.037 -- 7.1 42999 35363 0.0 0.0 43.2
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)
2.6 2.64 66.8 0.155 0.155 4.0 1.8 1412

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
FOURIER SYNTHESIS 2.6 30.0 0.0 0.0 43068 35355 1750 82.1 -- -- 0.209 0.271 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 2.6 2.72 3483 175 3308 0.288 0.283 0.021 65.6
X Ray Diffraction 2.72 2.86 3888 206 3682 0.264 0.256 0.018 73.2
X Ray Diffraction 2.86 3.04 4176 175 4001 0.261 0.257 0.019 78.2
X Ray Diffraction 3.04 3.28 4438 217 4221 0.245 0.247 0.017 83.0
X Ray Diffraction 3.28 3.61 4593 242 4351 0.22 0.227 0.015 86.0
X Ray Diffraction 3.61 4.13 4702 239 4463 0.18 0.184 0.012 87.2
X Ray Diffraction 4.13 5.19 4997 239 4758 0.156 0.156 0.01 92.2
X Ray Diffraction 5.19 29.72 5078 257 4821 0.219 0.218 0.014 90.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 45.48
Anisotropic B[1][1] -10.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -9.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 20.19
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 2.78
x_torsion_deg 23.4
x_angle_deg 1.6
x_bond_d 0.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.52
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8335
Nucleic Acid Atoms 0
Heterogen Atoms 233
Solvent Atoms 257

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
CNS phasing