7FDS | pdb_00007fds

High resolution crystal structure of LpqH from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	298	0.2M Ammonium sulphate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.9	α = 90
b = 78.51	β = 107.34
c = 42.18	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 PILATUS 6M		2021-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.258	28.557	99.1	0.061	0.067	0.078	0.047	0.997	10.1	4.5		49917

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.258	1.28	98		0.502	0.58	0.649	0.407	0.811

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	4ZJM	1.258	28.557	49888	2464	99.106	0.145	0.1429	0.15	0.1779	0.18	19.54

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]
2.045		0.358	-1.291		-0.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	51.07
r_dihedral_angle_3_deg	13.052
r_rigid_bond_restr	12.016
r_dihedral_angle_1_deg	6.742
r_scangle_it	5.824
r_scangle_other	5.821
r_lrange_it	5.529
r_lrange_other	5.515
r_scbond_it	4.727
r_scbond_other	4.723
r_mcangle_it	4.433
r_mcangle_other	4.433
r_mcbond_it	3.516
r_mcbond_other	3.514
r_angle_refined_deg	2.402
r_angle_other_deg	1.706
r_symmetry_nbd_refined	0.227
r_nbd_other	0.218
r_symmetry_nbd_other	0.2
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.117
r_symmetry_nbtor_other	0.093
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1527
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing