5IZD | pdb_00005izd

Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	20 mM glutamic acid (racemic), 20 mM glycine, 20 mM serine (racemic), 20 mM alanine (racemic), 20 mM lysine-HCl (racemic), 50 mM MOPS, 50 mM Sodium HEPES, pH 7.5; 20% Ethylene Glycol, 10% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.289	α = 90
b = 152.353	β = 92.19
c = 149.905	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	PIXEL	DECTRIS PILATUS 6M		2015-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.95	48.1	99.8	0.092	0.999	14.38	6.84		310836			37

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	1.95	2.06	98.9		1.98

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 (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	3K2W	2.05	48.1	253577	13347	99.94	0.17021	0.16838	0.18	0.2054	0.21	RANDOM	37.134

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]
2.47		-1.04	-2.5		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.763
r_dihedral_angle_4_deg	19.735
r_dihedral_angle_3_deg	13.529
r_dihedral_angle_1_deg	6.314
r_long_range_B_refined	6.092
r_long_range_B_other	6.061
r_angle_refined_deg	1.748
r_scangle_other	1.163
r_angle_other_deg	1.03
r_mcangle_it	0.753
r_mcangle_other	0.753
r_scbond_it	0.73
r_scbond_other	0.722
r_mcbond_it	0.439
r_mcbond_other	0.439
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30004
Nucleic Acid Atoms
Solvent Atoms	1353
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
BALBES	phasing
XDS	data scaling