7E3R | pdb_00007e3r

Crystal structure of TrmL from Vibrio vulnificus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KDZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	1M Tris-hydrochloride pH 8.5, 8% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.29	α = 90
b = 52.29	β = 90
c = 119.689	γ = 90

Symmetry
Space Group	P 41 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 EIGER X 9M		2020-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97957	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	50	99.4	0.08	0.084	0.025	7	10.7		16324

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	1.78	1.81	93.3		0.833	0.875	0.258	0.94		7.5

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	4KDZ	1.79	39.41	15402	860	98.73	0.2023	0.2	0.2136	0.2425	0.2472	RANDOM	40.292

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]
2.81			2.81		-5.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.091
r_dihedral_angle_4_deg	20.522
r_dihedral_angle_3_deg	13.788
r_dihedral_angle_1_deg	6.294
r_angle_refined_deg	1.581
r_angle_other_deg	1.341
r_chiral_restr	0.079
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	1139
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing