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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement