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_nbd_refined 0.272
r_angle_refined_deg 1.219
r_xyhbond_nbd_refined 0.097
r_symmetry_hbond_refined 0.161
r_dihedral_angle_1_deg 0.755
r_symmetry_vdw_refined 0.295
r_scangle_it 3.825
r_bond_refined_d 0.007
r_mcbond_it 0.544
r_scbond_it 2.331
r_mcangle_it 1.09
r_chiral_restr 0.075
r_gen_planes_refined 0.003
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHELXD phasing
SHARP phasing
REFMAC refinement version: 5.1.24