3GBR | pdb_00003gbr

Anthranilate phosphoribosyl-transferase (TRPD) double mutant D83G F149S from S. solfataricus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	18% PEG (w/v) 1500, 10% glycerol (v/v), 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.945	α = 90
b = 65.993	β = 98.81
c = 84.262	γ = 90

Symmetry
Space Group	P 1 21 1

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	PSI PILATUS 6M		2008-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.725	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.25	46.08	98.7	0.048	21.3	3.37		31695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.3	97.6		0.382	5.1	3.44	1996

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZYK	2.25	20	30691	1003	100	0.19383	0.19169	0.2	0.25954	0.26	RANDOM	24.986

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]
0.51		0.94	-1.59		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.853
r_dihedral_angle_3_deg	16.016
r_dihedral_angle_4_deg	15.233
r_scangle_it	8.542
r_scbond_it	6.755
r_dihedral_angle_1_deg	5.595
r_mcangle_it	4.187
r_mcbond_it	3.786
r_angle_other_deg	1.596
r_angle_refined_deg	1.16
r_mcbond_other	0.919
r_metal_ion_refined	0.34
r_symmetry_vdw_other	0.242
r_nbd_refined	0.187
r_chiral_restr	0.181
r_nbd_other	0.179
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.124
r_symmetry_vdw_refined	0.121
r_symmetry_hbond_refined	0.12
r_nbtor_other	0.088
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5237
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	74

Software

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