6YAJ | pdb_00006yaj

Split gene transketolase, inactive beta4 tetramer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.878	α = 90
b = 101.878	β = 90
c = 164.546	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.9	86.62	99.8	0.053	0.999	13.1	5.2		131289

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93			4.245	0.339

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1qgd	1.9	64.008	131176	6613	99.757	0.179	0.1776	0.18	0.2077	0.21	59.984

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.167			2.167		-4.333

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.746
r_dihedral_angle_4_deg	22.247
r_dihedral_angle_3_deg	17.756
r_lrange_it	12.015
r_scangle_it	9.853
r_scbond_it	7.1
r_mcangle_it	6.524
r_dihedral_angle_1_deg	5.125
r_mcbond_it	4.701
r_angle_refined_deg	1.605
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.143
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.105
r_ncsr_local_group_3	0.105
r_ncsr_local_group_6	0.097
r_ncsr_local_group_5	0.092
r_ncsr_local_group_4	0.09
r_ncsr_local_group_2	0.088
r_ncsr_local_group_1	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9005
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	103

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing