9GIG | pdb_00009gig

NMDA bound to compound 387

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
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.09	α = 90
b = 90.77	β = 90
c = 122.88	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 PILATUS3 X 6M		2018-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.09	46.47	100	0.242	0.292	0.152	0.964	4.3	6.4		36660			33.917

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	2.09	2.13	100		1.027	0.657	0.578	1.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.09	46.47	36598	1861	99.94	0.208	0.2058	0.2066	0.2566	0.2574	RANDOM	44.433

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]
-2.307			0.569		1.738

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.505
r_dihedral_angle_6_deg	14.269
r_lrange_it	9.653
r_lrange_other	9.653
r_scangle_it	7.551
r_scangle_other	7.55
r_dihedral_angle_1_deg	6.9
r_dihedral_angle_2_deg	6.769
r_mcangle_it	5.601
r_mcangle_other	5.6
r_scbond_it	5.118
r_scbond_other	5.118
r_mcbond_it	4.01
r_mcbond_other	4.01
r_angle_refined_deg	1.583
r_angle_other_deg	0.554
r_nbd_refined	0.217
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.177
r_symmetry_xyhbond_nbd_other	0.156
r_symmetry_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.08
r_bond_refined_d	0.008
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	4276
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	34

Software

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