9UAL | pdb_00009ual

Crystal structure of Trimucrin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7X4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.3M Zinc acetate, 25% PEG 3350, 0.1M Cacodylate, 5% Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.954	α = 90
b = 58.397	β = 90.266
c = 42.871	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		2024-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97625	NSRRC	TPS 07A

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	1.68	30	99.6	0.996	10.6	4.6		15133

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	1.68	1.78			0.836

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	1.68	29.22	15132	752	99.572	0.176	0.1739	0.184	0.2171	0.2251	20.981

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]
-0.523		-0.236	1.165		-0.639

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.237
r_dihedral_angle_4_deg	18.739
r_dihedral_angle_3_deg	14.281
r_dihedral_angle_1_deg	7.146
r_lrange_it	5.848
r_lrange_other	5.848
r_scangle_it	3.961
r_scangle_other	3.959
r_mcangle_it	2.879
r_mcangle_other	2.876
r_scbond_it	2.528
r_scbond_other	2.526
r_mcbond_it	1.81
r_mcbond_other	1.674
r_angle_refined_deg	1.449
r_angle_other_deg	1.338
r_nbd_refined	0.229
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.16
r_nbd_other	0.156
r_nbtor_refined	0.153
r_metal_ion_refined	0.084
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.022
r_gen_planes_refined	0.013
r_bond_refined_d	0.009
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1042
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	26

Software

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