2J24 | pdb_00002j24

The functional role of the conserved active site proline of triosephosphate isomerase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TIM	PDB ENTRY 5TIM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		WELL SOLUTION: 0.1 M TEA PH 7.0, 27% PEG 2K MME AND 0.2 M KSCN PROTEIN SOLUTION: 11 MG/ML PROTEIN, 0.02 M TRIS/HCL PH 7.0, 0.1 M NACL, 1 MM DTT, 1 MM EDTA AND 1 MM NAN3.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.5	α = 80.49
b = 43.72	β = 79.61
c = 71.27	γ = 64.66

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 345 mm plate	MONTEL MIRRORS	2004-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	2.1	25	94.5	0.07	13.8	2.65		22102			17.7

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	2.1	2.2	92.2		0.13	8.67	2.63

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 5TIM	2.1	19.21	20995	1106	100	0.153	0.149	0.16	0.23	0.24	RANDOM	7.11

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]
0.3	0.12	0.21	0.15	-0.79	-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.228
r_dihedral_angle_3_deg	16.431
r_dihedral_angle_4_deg	13.964
r_dihedral_angle_1_deg	7.264
r_scangle_it	2.567
r_scbond_it	1.833
r_angle_refined_deg	1.638
r_mcangle_it	1.008
r_angle_other_deg	0.88
r_mcbond_it	0.792
r_symmetry_vdw_other	0.233
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.201
r_nbd_other	0.192
r_nbtor_refined	0.182
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.097
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3762
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing