3M1P | pdb_00003m1p

Structure of ribose 5-phosphate isomerase type B from Trypanosoma cruzi, soaked with allose-6-phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	20% PEG3350, 0.2M sodium acetate, 0.1 M BIS-TRIS propane, pH 8.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.763	α = 90
b = 92.763	β = 90
c = 93.094	γ = 90

Symmetry
Space Group	P 42 21 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	ADSC QUANTUM 315r		2009-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	65.71	90.1	0.105	0.105	16.3	6.5	18940	18940

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)
	2.2	2.32	92.6		0.268	0.268	2.8	6.5	2802

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.2	30	18909	978	89.11	0.189	0.187	0.19	0.232	0.23	RANDOM	21.072

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]
0.67			0.67		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.906
r_dihedral_angle_4_deg	19.061
r_dihedral_angle_3_deg	12.61
r_dihedral_angle_1_deg	5.134
r_scangle_it	2.393
r_scbond_it	1.469
r_angle_refined_deg	1.128
r_mcangle_it	1.002
r_mcbond_it	0.592
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.906
r_dihedral_angle_4_deg	19.061
r_dihedral_angle_3_deg	12.61
r_dihedral_angle_1_deg	5.134
r_scangle_it	2.393
r_scbond_it	1.469
r_angle_refined_deg	1.128
r_mcangle_it	1.002
r_mcbond_it	0.592
r_nbtor_refined	0.297
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.179
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.