7P1Y | pdb_00007p1y

A small alarmone hydrolase TdActApo2 mutant - T78N

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GNI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.22 mM TdRel-D78N protein in the buffer of 1 mM MnCl2, 25 mM Tris-HCl pH 8.0, and 200 mM NaCl was mixed 1:1 ratio with the precipitant containing 0.2 M NH4Cl and 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.286	α = 90
b = 69.189	β = 93.015
c = 132.07	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	DECTRIS EIGER2 X 16M		2021-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976238	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.38	61.345	100	0.999	10.4	11.7		44562

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.39	2.47	100		0.604	1	11.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3gni	2.38	61.278	44544	2212	99.978	0.193	0.1907	0.2	0.2269	0.23	63.939

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]
4.215		-0.998	-0.017		-4.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.488
r_dihedral_angle_4_deg	21.442
r_dihedral_angle_3_deg	17.968
r_lrange_it	12.855
r_lrange_other	12.841
r_scangle_it	10.131
r_scangle_other	10.13
r_mcangle_it	9.43
r_mcangle_other	9.43
r_scbond_it	6.996
r_scbond_other	6.995
r_mcbond_other	6.629
r_mcbond_it	6.628
r_dihedral_angle_1_deg	6.242
r_angle_refined_deg	1.64
r_angle_other_deg	1.37
r_symmetry_nbd_refined	0.402
r_symmetry_xyhbond_nbd_refined	0.382
r_nbd_refined	0.231
r_nbd_other	0.188
r_symmetry_nbd_other	0.17
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.167
r_ncsr_local_group_6	0.086
r_ncsr_local_group_3	0.084
r_ncsr_local_group_5	0.083
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_2	0.082
r_ncsr_local_group_1	0.08
r_ncsr_local_group_4	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5493
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing