1SPQ | pdb_00001spq

Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TIM	PDB ENTRY 8TIM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.1	277	PEG 6000, Tris, 2-phosphoglycolate, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.706	α = 90
b = 57.334	β = 92.89
c = 106.154	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARRESEARCH	Bent mirror	2003-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8	EMBL/DESY, HAMBURG	X11

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	2.13	40	97.8	0.057	0.062	22	3.48	25864	25268			23.9

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	2.13	2.21	78.8		0.145	0.144	7.4		2035

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 8TIM	2.16	38.35	25268	23998	1270	96.05	0.16215	0.16215	0.16023	0.17	0.19779	0.21	RANDOM	11.296

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]
-1.19		0.92	-1.29		2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.931
r_mcangle_it	1.588
r_scangle_it	1.507
r_angle_refined_deg	1.225
r_mcbond_it	0.983
r_scbond_it	0.962
r_angle_other_deg	0.858
r_symmetry_vdw_other	0.276
r_nbd_other	0.221
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.12
r_nbtor_other	0.079
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3664
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing