9SQF | pdb_00009sqf

PaMurU in complex with Mn2+ and UTP substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HHD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.943	α = 89.885
b = 51.957	β = 89.557
c = 73.117	γ = 77.559

Symmetry
Space Group	P 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 PILATUS 6M		2025-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.7712	ALBA	XALOC

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	2.1	50.74	93.8	0.121	0.978	8.3	3.5		40882

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	2.1	2.16	89.9		0.423	0.708	1.3	3.5

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	2.1	50.74	40875	1921	93.827	0.204	0.2012	0.2093	0.2515	0.2581	28.569

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]
0.399	0.503	-1.098	-0.169	0.945	-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.341
r_dihedral_angle_3_deg	12.941
r_dihedral_angle_2_deg	7.098
r_dihedral_angle_1_deg	6.997
r_lrange_other	6.037
r_lrange_it	6.035
r_scangle_it	4.104
r_scangle_other	4.104
r_mcangle_it	3.441
r_mcangle_other	3.441
r_scbond_it	2.631
r_scbond_other	2.631
r_mcbond_it	2.224
r_mcbond_other	2.221
r_angle_refined_deg	1.732
r_angle_other_deg	0.562
r_nbd_refined	0.223
r_symmetry_nbd_other	0.204
r_nbd_other	0.196
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.092
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5122
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	93

Software

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