3SDW

Crystal structure of a ribose-5-phosphate isomerase B RpiB from Coccidioides immitis bound to phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	CoimA.00584.a.A1 PS00647 at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2 against PACT screen condition A2 0.1 M SPG buffer pH 5.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 222975a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.7	α = 90
b = 85.22	β = 90
c = 96.29	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	2011-05-24	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	1.8	50	99.8	0.119	12.3	3.6	28652			-3	19.61

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	1.8	1.85	98.8		0.438	2.08	2	2133

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3qd5	1.8	30.24	14922	752	99.47	0.15	0.1486	0.1762	RANDOM	13.1584

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]
-0.28			0.72		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.981
r_dihedral_angle_4_deg	11.876
r_dihedral_angle_3_deg	10.645
r_dihedral_angle_1_deg	5.142
r_scangle_it	3.313
r_scbond_it	1.996
r_angle_refined_deg	1.288
r_mcangle_it	1.069
r_mcbond_it	0.633
r_chiral_restr	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1179
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	14

Software

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