X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details ammonium sulfate, hepes, sucrose, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 203.25 α = 90
b = 203.25 β = 90
c = 42.81 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.9795 NSLS X4A

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
3.2 30 99.9 -- -- -- -- -- 8610 -- -- --
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)
3.2 3.31 100.0 -- -- -- -- --

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 3.2 30.0 -- 0.0 -- 8536 433 98.56 0.213 -- 0.211 0.247 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 3.2 3.278 -- 38 582 0.298 0.486 -- 94.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 74.397
Anisotropic B[1][1] 0.64
Anisotropic B[1][2] 0.32
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.96
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 7.332
r_gen_planes_refined 0.005
r_chiral_restr 0.114
r_dihedral_angle_3_deg 23.83
r_scbond_it 1.542
r_angle_refined_deg 1.764
r_metal_ion_refined 0.201
r_mcangle_it 1.131
r_dihedral_angle_2_deg 37.984
r_dihedral_angle_4_deg 18.619
r_mcbond_it 0.626
r_nbtor_refined 0.328
r_scangle_it 2.683
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.232
r_symmetry_vdw_refined 0.23
r_symmetry_hbond_refined 0.208
r_nbd_refined 0.257
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1612
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 15

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.700
DENZO data reduction
CCP4 data scaling version: (SCALA)
PHASER phasing