1SSG | pdb_00001ssg

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	5.5	294	Citrate, ammonium sulphate, sodium chloride, 2-phosphoglycolate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3	59.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.327	α = 90
b = 88.327	β = 90
c = 163.874	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	MARRESEARCH	Focusing mirror	2002-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS	1.5

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	2.8	20	99.7	0.089	0.11	25	5.11	16713	16663			21.4

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	2.8	2.9	97.4		0.6	0.74	3.4		1622

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	2.9	19.96	14272	13881	727	97.26	0.20663	0.20663	0.20473	0.18	0.24433	0.24	RANDOM	14.592

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]
1.57			1.57		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.645
r_scangle_it	1.532
r_angle_other_deg	1.329
r_angle_refined_deg	1.328
r_scbond_it	0.944
r_mcangle_it	0.509
r_symmetry_vdw_other	0.302
r_mcbond_it	0.278
r_nbd_other	0.247
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.123
r_nbtor_other	0.09
r_chiral_restr	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3742
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	56

Software

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