3K7P | pdb_00003k7p

Structure of mutant of ribose 5-phosphate isomerase type B from Trypanosoma cruzi.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NN4	pdb entry 1NN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	293	0.8 M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.079	α = 90
b = 93.079	β = 90
c = 93.827	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 210		2008-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	1.4	30	98.2	0.097	0.097	11.1	5.7		79637

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)
1	1.4	1.48	100		0.335	0.335	3.1	5.7	11693

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 (All)	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 1NN4	1.4	30	79570	3977	97.78	0.223	0.223	0.223	0.22	0.232	0.23	RANDOM	16.949

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]
0.31			0.31		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.721
r_dihedral_angle_4_deg	16.608
r_dihedral_angle_3_deg	11.612
r_dihedral_angle_1_deg	4.304
r_scangle_it	1.943
r_scbond_it	1.2
r_angle_refined_deg	0.943
r_mcangle_it	0.823
r_mcbond_it	0.488
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.721
r_dihedral_angle_4_deg	16.608
r_dihedral_angle_3_deg	11.612
r_dihedral_angle_1_deg	4.304
r_scangle_it	1.943
r_scbond_it	1.2
r_angle_refined_deg	0.943
r_mcangle_it	0.823
r_mcbond_it	0.488
r_nbtor_refined	0.299
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.176
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.083
r_chiral_restr	0.071
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
SCALA	data scaling

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.