X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 2.5M sodium chloride, 0.03M phosphate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.6 α = 90
b = 61 β = 90
c = 33.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC double-mirror 1999-04-07
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
1.9 41.5 88.1 0.078 -- -- -- 20728 8599 -- -- --

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
MOLECULAR REPLACEMENT 1.9 41.5 -- -- -- 8185 410 88.14 -- 0.17082 0.16746 0.23541 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 1.9 1.949 -- 26 484 0.235 0.328 -- 72.34
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 13.927
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.776
r_mcangle_it 1.362
r_metal_ion_refined 0.103
r_scangle_it 4.22
r_symmetry_vdw_refined 0.188
r_nbd_refined 0.222
r_angle_refined_deg 1.522
r_nbtor_refined 0.299
r_dihedral_angle_1_deg 6.436
r_scbond_it 2.539
r_dihedral_angle_4_deg 13.213
r_dihedral_angle_3_deg 13.376
r_gen_planes_refined 0.006
r_bond_refined_d 0.014
r_symmetry_hbond_refined 0.223
r_xyhbond_nbd_refined 0.177
r_dihedral_angle_2_deg 34.976
r_chiral_restr 0.108
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1029
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 131

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing