X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.1
Temperature 294.0
Details 0.4M (NH4)H2PO4, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.7 α = 90
b = 96.74 β = 90
c = 192.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Double focusing X-ray optics 2002-11-06
CCD MARRESEARCH -- 2005-09-18
Diffraction Radiation
Monochromator Protocol
-- MAD
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 0.9792, 0.9795 MPG/DESY, HAMBURG BW6
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05, 0.900, 0.9198, 0.9200 MPG/DESY, HAMBURG BW6

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
1.7 40 97.7 0.043 0.043 -- 3.3 158490 158490 -- -- 31.0
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)
1.7 1.72 92.6 0.34 0.34 3.9 3.0 5907

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 1.7 20.0 -- -- 157798 157798 7898 97.5 0.208 0.208 0.207 0.236 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 1.7 1.73 10104 499 9078 0.25 0.32 -- 92.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 20.1
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.98
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.39
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.4
r_dihedral_angle_1_deg 5.09
r_dihedral_angle_3_deg 15.312
r_symmetry_vdw_refined 0.288
r_mcbond_it 1.18
r_dihedral_angle_4_deg 17.786
r_symmetry_hbond_refined 0.241
r_bond_refined_d 0.012
r_chiral_restr 0.095
r_scbond_it 2.591
r_mcangle_it 1.463
r_angle_refined_deg 1.475
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.152
r_dihedral_angle_2_deg 33.589
r_nbd_refined 0.222
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9695
Nucleic Acid Atoms 726
Heterogen Atoms 0
Solvent Atoms 602

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
DENZO data reduction
SCALEPACK data scaling
SHELXD phasing
SHELXE model building
MLPHARE phasing
GETAX phasing
DM phasing