2GEK | pdb_00002gek

Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	10 MG/ML PIMA, 1 mM GDP, 10-18% PEG 8000, 200 mM CALCIUM ACETATE, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.176	α = 90
b = 72.425	β = 90
c = 138.23	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2004-06-13	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH		2005-07-31	M	MAD
3	1
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934000	ESRF	ID14-1
2	SYNCHROTRON	SLS BEAMLINE X06SA	0.979106, 0.979261, 0.97181	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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
1,2	2.4	37.165	99.7	0.058	0.058	9	3.4	15229	15229	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.4	2.53	100	100	0.313	0.313	2.4	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	2.4	29.827	15202	15202	1090	99.47	0.196	0.196	0.191	0.19	0.259	0.26	RANDOM	36.819

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]
1.21			-0.94		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.634
r_dihedral_angle_4_deg	19.226
r_dihedral_angle_3_deg	18.446
r_dihedral_angle_1_deg	6.694
r_scangle_it	3.426
r_scbond_it	2.263
r_angle_refined_deg	1.857
r_mcangle_it	1.279
r_mcbond_it	0.863
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.634
r_dihedral_angle_4_deg	19.226
r_dihedral_angle_3_deg	18.446
r_dihedral_angle_1_deg	6.694
r_scangle_it	3.426
r_scbond_it	2.263
r_angle_refined_deg	1.857
r_mcangle_it	1.279
r_mcbond_it	0.863
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.123
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2656
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.