5ZT4 | pdb_00005zt4

Crystal structure of H99A mutant of phosphomannose isomerase from Salmonella typhimurium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H1M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.8	298	0.1 M Magnesium acetate tetrahydrate, 0.2 M Sodium cacodylate pH 6.8, 20% PEG 8000,5% dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.22	α = 90
b = 91.66	β = 90
c = 116.23	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	MARMOSAIC 225 mm CCD		2015-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95372	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	32.35	100	0.095	15.9	12.7		43599

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79			0.795

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	3H1M	1.7	32.35	41332	2189	99.93	0.18183	0.18003	0.19	0.21552	0.22	RANDOM	27.04

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]
-1.28			-1.07		2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.113
r_dihedral_angle_4_deg	13.144
r_dihedral_angle_3_deg	11.723
r_dihedral_angle_1_deg	6.732
r_long_range_B_other	5.926
r_long_range_B_refined	5.923
r_scangle_other	3.207
r_scbond_it	2.202
r_scbond_other	2.187
r_mcangle_it	1.968
r_mcangle_other	1.967
r_angle_refined_deg	1.848
r_mcbond_it	1.34
r_mcbond_other	1.339
r_angle_other_deg	0.863
r_chiral_restr	0.11
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2943
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing