9H70 | pdb_00009h70

Crystal structure of LMTP1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2LT2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283	CaCl2, HEPES/KOH, PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.93	α = 90
b = 93.93	β = 90
c = 52.378	γ = 120

Symmetry
Space Group	P 32 2 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		2024-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.98	ESRF	BM07

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.69	47.01	100	0.31809	5.3	8.3		57890

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	1.69	1.89			0.69

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	1.69	47.009	30079	1482	99.9	0.32	0.3181	0.3226	0.3655	0.3667	23.924

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]
0.361	0.18		0.361		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.82
r_dihedral_angle_6_deg	15.398
r_dihedral_angle_2_deg	11.305
r_dihedral_angle_1_deg	6.976
r_lrange_other	6.317
r_lrange_it	6.31
r_scangle_it	4.405
r_scangle_other	4.403
r_mcangle_it	3.478
r_mcangle_other	3.477
r_scbond_it	3.014
r_scbond_other	3.012
r_mcbond_other	2.44
r_mcbond_it	2.436
r_angle_refined_deg	1.724
r_angle_other_deg	0.562
r_symmetry_nbd_refined	0.391
r_nbd_other	0.285
r_nbd_refined	0.233
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.186
r_metal_ion_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1199
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MrBUMP	phasing