1SQ7 | pdb_00001sq7

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

X-RAY DIFFRACTION

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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	5.2	295	PEG 6000, citrate, t-butanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.67	α = 90
b = 61.67	β = 90
c = 500.886	γ = 120

Symmetry
Space Group	P 61 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	MARRESEARCH	Bent mirror	2002-06-15	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)	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	2.8	30	94.3	0.083	10.42	6.62	16236	15311			20.4

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	2.76	2.93	82.4		0.117	7	5.29	2572

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	2.85	28.28	13977	13279	698	100	0.20468	0.20468	0.20214	0.19	0.25185	0.24	RANDOM	3.209

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]
1.41	0.71		1.41		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.193
r_angle_refined_deg	1.074
r_angle_other_deg	0.837
r_scangle_it	0.488
r_scbond_it	0.293
r_nbd_other	0.212
r_symmetry_vdw_other	0.171
r_mcangle_it	0.165
r_nbd_refined	0.159
r_xyhbond_nbd_refined	0.133
r_symmetry_vdw_refined	0.099
r_mcbond_it	0.089
r_symmetry_hbond_refined	0.082
r_nbtor_other	0.078
r_chiral_restr	0.05
r_bond_refined_d	0.01
r_bond_other_d	0.003
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3744
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms

Software

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