X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 5-15% PEG 4000, 0.2 M sodium acetate, 0.1 M cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.64 α = 90
b = 72.67 β = 104.52
c = 62.06 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-12-03
Diffraction Radiation
Monochromator Protocol
double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393, 0.9506, 0.9393 ESRF ID14-4

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
1.55 31.01 99.8 0.085 -- -- 4.1 -- 53094 -3.0 -3.0 --
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)
1.55 1.63 99.8 0.4 -- 2.5 4.1 7734

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
MAD 1.55 31.01 -- -3.0 50407 50407 2659 99.81 0.17592 0.17592 0.17412 0.21142 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 1.55 1.59 3275 212 3663 0.231 0.283 -- 99.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.622
Anisotropic B[1][1] 0.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.75
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.084
r_symmetry_vdw_refined 0.286
r_angle_refined_deg 1.367
r_xyhbond_nbd_refined 0.149
r_dihedral_angle_2_deg 34.09
r_nbd_other 0.194
r_nbtor_other 0.087
r_angle_other_deg 0.944
r_nbd_refined 0.237
r_mcbond_it 0.882
r_dihedral_angle_4_deg 22.051
r_scangle_it 4.312
r_gen_planes_refined 0.006
r_bond_other_d 0.001
r_mcbond_other 0.258
r_gen_planes_other 0.001
r_scbond_it 2.676
r_bond_refined_d 0.014
r_nbtor_refined 0.182
r_dihedral_angle_3_deg 13.613
r_dihedral_angle_1_deg 4.105
r_symmetry_vdw_other 0.321
r_symmetry_hbond_refined 0.153
r_mcangle_it 1.614
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.079
Luzzati Sigma A (Observed) 0.051
Luzzati ESD (R-Free Set) 0.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2702
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 427

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MLPHARE phasing