5M8H | pdb_00005m8h

ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VD2	2VD2, 3OD1
experimental model	PDB	3OD1	2VD2, 3OD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	11% PEG3350, 0.1M bicine pH8.5, 0.15M strontium chloride, 0.15M potassium bromide, 4% 1,6-hexanediol

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.02	α = 90
b = 146.73	β = 102.4
c = 101.9	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	CCD	RIGAKU SATURN 944+	varimax mirrors	2016-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.34	30.63	97.6	0.135	0.994	6.3	3.5		110587

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.38	81		0.969	0.366		2.4

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	2VD2, 3OD1	2.34	30.63	105092	5467	97.47	0.2295	0.2274	0.2327	0.2689	0.2739	RANDOM	47.653

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]
-1.77		0.34	-0.22		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.537
r_dihedral_angle_4_deg	19.01
r_dihedral_angle_3_deg	15.29
r_dihedral_angle_1_deg	6.134
r_mcangle_it	4.738
r_mcbond_it	2.975
r_mcbond_other	2.974
r_angle_refined_deg	1.438
r_angle_other_deg	0.943
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18206
Nucleic Acid Atoms
Solvent Atoms	629
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing