5OFM

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.1 M PCTP, pH 7, 23-25 % PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.342	α = 97.91
b = 45.86	β = 110.74
c = 56.175	γ = 106.39

Symmetry
Space Group	P 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 PILATUS3 S 6M		2014-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.917	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.5	50.66	86.4	0.064	0.058	0.99	6.3	2.1		51430

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	86.3		0.376	0.344	0.804		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	50.66	48623	2653	84.73	0.19415	0.19118	0.24917	RANDOM	15.757

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]
0.27	0.19	-0.7	-0.76	-0.18	0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.676
r_sphericity_free	32.417
r_dihedral_angle_4_deg	20.688
r_dihedral_angle_3_deg	17.043
r_sphericity_bonded	12.662
r_dihedral_angle_1_deg	7.035
r_long_range_B_refined	4.591
r_long_range_B_other	4.591
r_scangle_other	3.718
r_scbond_it	3.274
r_scbond_other	3.274
r_mcangle_it	3.259
r_mcangle_other	3.259
r_rigid_bond_restr	3.158
r_mcbond_it	2.874
r_mcbond_other	2.462
r_angle_refined_deg	2.155
r_angle_other_deg	1.157
r_chiral_restr	0.139
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2920
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing