8PRU | pdb_00008pru

Engineered form of T thermophiles AHIR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.03	α = 90
b = 142.72	β = 90
c = 126.13	γ = 90

Symmetry
Space Group	P 21 21 2

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		2012-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.89	63.06	94.7	0.154	0.177	0.085	0.993	5.6	4		184696

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92	96.8		1.122	1.298	0.637	0.679	1.5	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	63.06	161433	8715	97.45	0.26	0.2589	0.2616	0.2884	0.2904	46.788

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]
0.829			0.781		-1.611

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.875
r_dihedral_angle_2_deg	16.468
r_dihedral_angle_6_deg	15.437
r_lrange_other	9.972
r_lrange_it	9.97
r_scangle_it	8.185
r_scangle_other	8.183
r_mcangle_it	6.952
r_mcangle_other	6.952
r_dihedral_angle_1_deg	6.578
r_scbond_it	5.707
r_scbond_other	5.706
r_mcbond_it	5.117
r_mcbond_other	5.116
r_angle_refined_deg	1.449
r_angle_other_deg	0.481
r_metal_ion_refined	0.231
r_nbd_refined	0.23
r_symmetry_nbd_other	0.191
r_nbd_other	0.185
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.065
r_ncsr_local_group_6	0.032
r_ncsr_local_group_11	0.031
r_ncsr_local_group_10	0.03
r_ncsr_local_group_2	0.028
r_ncsr_local_group_12	0.028
r_ncsr_local_group_7	0.026
r_ncsr_local_group_9	0.025
r_ncsr_local_group_1	0.024
r_ncsr_local_group_4	0.024
r_ncsr_local_group_8	0.024
r_ncsr_local_group_3	0.023
r_ncsr_local_group_13	0.023
r_ncsr_local_group_15	0.023
r_ncsr_local_group_14	0.022
r_ncsr_local_group_5	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14460
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	25

Software

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