X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 277.0
Details MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.94 α = 90
b = 30.79 β = 109.31
c = 113.08 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-07-03
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.946 SSRL BL9-1

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
1.75 53 98.1 0.11 -- -- 5.4 33765 33157 0.0 0.0 23.8
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)
1.75 1.81 94.7 0.291 -- 4.1 3.2 3174

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
SAD 1.75 53.0 0.0 0.0 33594 33157 3312 98.16 0.21437 0.21437 0.21344 0.2228 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 1.75 1.795 2327 215 2112 0.253 0.244 -- 94.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.271
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.71
Anisotropic B[2][2] -0.94
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.45
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.825
r_bond_refined_d 0.007
r_angle_refined_deg 1.219
r_dihedral_angle_1_deg 0.755
r_chiral_restr 0.075
r_gen_planes_refined 0.003
r_nbd_refined 0.272
r_xyhbond_nbd_refined 0.097
r_symmetry_vdw_refined 0.295
r_symmetry_hbond_refined 0.161
r_mcbond_it 0.544
r_mcangle_it 1.09
r_scbond_it 2.331
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.222
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1311
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 149

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHELXD, SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SHELXD/SHARP model building
SCALEPACK data reduction
DENZO data collection