4GH0 | pdb_00004gh0

Crystal structure of D48V mutant of human GLTP bound with 12:0 monosulfatide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	15% PEG 3350, 0.1M MES pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.984	α = 90
b = 47.242	β = 125.52
c = 62.193	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	ADSC QUANTUM 315r		2009-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9754	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.35	50	99.8			69954	40558	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	99.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	3S0I	1.35	15	2	40407	38442	1965	99.79	0.15359	0.15359	0.15215	0.16	0.18078	0.15	RANDOM	20.404

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]
-0.82		-0.48	-0.08		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.025
r_dihedral_angle_3_deg	12.468
r_dihedral_angle_4_deg	11.354
r_sphericity_free	5.786
r_dihedral_angle_1_deg	5.426
r_scangle_it	4.229
r_sphericity_bonded	4.128
r_scbond_it	3.333
r_mcangle_it	2.25
r_mcbond_it	1.911
r_rigid_bond_restr	1.839
r_angle_refined_deg	1.602
r_angle_other_deg	1.273
r_mcbond_other	0.729
r_symmetry_vdw_other	0.32
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.212
r_nbtor_refined	0.192
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.094
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.043
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1611
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	64

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling