1SSD | pdb_00001ssd

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, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.422	α = 90
b = 88.422	β = 90
c = 161.874	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	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	2.9	19.73	98.8	0.105	0.095	15.1	5.41	20463	20217			31.1

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	2.9		99.4		0.298	0.355	7.1		2007

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	19.7	14760	13996	764	99.24	0.15794	0.15794	0.15611	0.16	0.19287	0.19	RANDOM	25.34

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]
0.02			0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.04
r_scangle_it	1.684
r_angle_refined_deg	1.188
r_scbond_it	0.938
r_angle_other_deg	0.76
r_mcangle_it	0.537
r_mcbond_it	0.261
r_nbd_other	0.229
r_symmetry_vdw_other	0.228
r_xyhbond_nbd_refined	0.218
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.109
r_symmetry_hbond_refined	0.097
r_nbtor_other	0.084
r_chiral_restr	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3742
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing