3GPS | pdb_00003gps

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 5.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DGD	PDB entry 3DGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.495	α = 90
b = 61.615	β = 90.01
c = 47.268	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2008-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458	LNLS	W01B-MX2

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	1.78	27.9	99.18	0.191	8.1	5.2		45854			31.6

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)
	1.78	1.82	100		0.488	3	5.1	6075

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 (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 3DGD	1.78	27.9	43051	2697	99.18	0.2023	0.20508	0.20205	0.215	0.2539	0.256	RANDOM	28.895

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]
0.33			0.58		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.892
r_dihedral_angle_3_deg	16.962
r_dihedral_angle_4_deg	16.888
r_sphericity_free	9.772
r_dihedral_angle_1_deg	7.782
r_scangle_it	5.253
r_sphericity_bonded	4.275
r_scbond_it	3.506
r_mcangle_it	2.699
r_angle_refined_deg	1.9
r_rigid_bond_restr	1.895
r_mcbond_it	1.692
r_angle_other_deg	1.016
r_mcbond_other	0.773
r_chiral_restr	0.117
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3551
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	94

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling