X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.75
Temperature 293.0
Details PEG 400, TRIS, OCTYL-BETA-D-GLUCOPYRANOSIDE, SODIUM AZIDE, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.78 α = 90
b = 124.14 β = 90
c = 129.61 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
IMAGE PLATE RIGAKU RAXIS IV -- 2002-01-25
Diffraction Radiation
Monochromator Protocol
Osmic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
2.15 33.2 98.7 -- 0.048 -- 10.7 24593 24593 0.0 0.0 32.2
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)
2.15 2.28 93.7 -- 0.367 2.1 8.2 3266

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
SIRAS 2.15 33.0 -- 0.0 24591 24591 1253 98.69 0.19093 0.19093 0.18951 0.21747 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 2.15 2.206 1619 74 1545 0.244 0.337 -- 89.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.491
Anisotropic B[1][1] 1.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.11
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_angle_refined_deg 1.719
r_scangle_it 4.702
r_chiral_restr 0.117
r_angle_other_deg 0.539
r_nbd_refined 0.214
r_gen_planes_refined 0.008
r_xyhbond_nbd_refined 0.147
r_scbond_it 2.973
r_mcbond_it 1.049
r_bond_refined_d 0.021
r_nbd_other 0.287
r_dihedral_angle_1_deg 5.519
r_mcbond_other 0.032
r_bond_other_d 0.001
r_symmetry_hbond_refined 0.132
r_nbtor_refined 0.308
r_symmetry_vdw_refined 0.25
r_dihedral_angle_4_deg 14.684
r_dihedral_angle_2_deg 43.917
r_dihedral_angle_3_deg 15.199
r_nbtor_other 0.239
r_mcangle_it 1.632
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.186
Luzzati Sigma A (Observed) 0.102
Luzzati Resolution Cutoff (Low) 33.0
Luzzati ESD (R-Free Set) 0.159
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2371
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 164

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0003
MOSFLM data reduction
CCP4 data scaling version: (TRUNCATE)
SHARP phasing