3SGW | pdb_00003sgw

Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SDW	pdb entry 3SDW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection reagent, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.46	α = 90
b = 84.42	β = 90
c = 96.17	γ = 90

Symmetry
Space Group	F 2 2 2

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+	VariMax	2011-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	1.7	50	94.5	0.044	34.74	9.6	17530	16561		-3	20.011

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	1.7	1.74	80.2		0.256	6.62	5.3	1281

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	pdb entry 3SDW	1.7	49.08	16509	832	94.19	0.1438	0.1421	0.15	0.1749	0.14	RANDOM	13.745

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]
-0.26			0.68		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.788
r_dihedral_angle_3_deg	10.199
r_dihedral_angle_4_deg	6.074
r_dihedral_angle_1_deg	5.1
r_scangle_it	3.535
r_scbond_it	2.024
r_angle_refined_deg	1.323
r_mcangle_it	1.119
r_mcbond_it	0.641
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.788
r_dihedral_angle_3_deg	10.199
r_dihedral_angle_4_deg	6.074
r_dihedral_angle_1_deg	5.1
r_scangle_it	3.535
r_scbond_it	2.024
r_angle_refined_deg	1.323
r_mcangle_it	1.119
r_mcbond_it	0.641
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	17

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.