X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 289.0
Details 0.1M Na(OAC), 27% PEG2KMME, 5mM FMN, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.03 α = 90
b = 87.18 β = 90
c = 94.98 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-12-19
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID

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
1.89 50 99.0 -- 0.087 -- 5.0 18453 18268 -- -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)
1.89 1.96 92.9 0.182 -- 12.8 4.6 1685

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 1.9 47.51 -- 0.0 17063 17063 919 99.66 0.17988 0.17988 0.17771 0.22054 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 -- 66 1233 0.159 0.246 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.295
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.88
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.541
r_dihedral_angle_1_deg 5.707
r_nbd_refined 0.214
r_symmetry_vdw_refined 0.187
r_bond_refined_d 0.017
r_angle_refined_deg 1.422
r_dihedral_angle_2_deg 33.203
r_chiral_restr 0.098
r_scbond_it 3.026
r_gen_planes_refined 0.008
r_mcbond_it 1.468
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.183
r_dihedral_angle_3_deg 13.665
r_symmetry_hbond_refined 0.254
r_scangle_it 4.338
r_dihedral_angle_4_deg 10.819
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1595
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 216

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-2000 data scaling
HKL-3000 phasing
SHELXE model building
SOLVE phasing
RESOLVE phasing
ARP/wARP model building