3PM6 | pdb_00003pm6

Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	23.4 mg/mL CoimA.00345.a.A1 PS00465 against ProPlex screen condition E11, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, soaked into 1 M NaI, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, 20% ethylene glycol, crystal tracking ID 206915e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.91	α = 90
b = 77.77	β = 93.71
c = 68.32	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	CCD	RIGAKU SATURN 944	Osmic VariMax HF	2010-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.2	50	97.5	0.104	12.96	7.3	30826	30048		-3	34.628

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	82.8		0.478	3.7	6	2254

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	SAD WITH MR	THROUGHOUT	2isv	2.2	50	30008	1505	97.35	0.1998	0.1978	0.2	0.2369	0.21	RANDOM	27.6569

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]
-0.5		1.32	-0.76		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.496
r_dihedral_angle_4_deg	22.928
r_dihedral_angle_3_deg	14.998
r_dihedral_angle_1_deg	5.506
r_scangle_it	3.425
r_scbond_it	2.11
r_angle_refined_deg	1.428
r_mcangle_it	1.298
r_mcbond_it	0.708
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.496
r_dihedral_angle_4_deg	22.928
r_dihedral_angle_3_deg	14.998
r_dihedral_angle_1_deg	5.506
r_scangle_it	3.425
r_scbond_it	2.11
r_angle_refined_deg	1.428
r_mcangle_it	1.298
r_mcbond_it	0.708
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4114
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	35

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.