9GIB

NMDA bound to compound 380

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	282.15	10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.972	α = 90
b = 90.036	β = 90
c = 123.174	γ = 90

Symmetry
Space Group	P 21 21 21

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-F		2018-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	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	1.948	72.7	100	0.143	0.061	0.996	8.2	6.4		44610

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	1.95	2	100		0.823	0.37	0.613	2.2	5.9

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.948	72.7	44423	2309	99.46	0.206	0.2032	0.2564	RANDOM	29.563

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]
-0.639			-0.37		1.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.222
r_dihedral_angle_6_deg	14.069
r_dihedral_angle_3_deg	13.742
r_lrange_it	7.692
r_lrange_other	7.692
r_dihedral_angle_1_deg	6.797
r_scangle_it	4.874
r_scangle_other	4.873
r_mcangle_it	4.151
r_mcangle_other	4.15
r_scbond_other	3.175
r_scbond_it	3.173
r_mcbond_it	2.627
r_mcbond_other	2.627
r_angle_refined_deg	1.494
r_angle_other_deg	0.507
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.176
r_nbd_other	0.175
r_symmetry_nbd_other	0.172
r_chiral_restr_other	0.163
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4302
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing