2GAO | pdb_00002gao

Crystal Structure of Human SAR1a in Complex With GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F6B	PDB Entry: 1F6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	30% PEG8000, 0.2M ammonium sulfate, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.295	α = 90
b = 63.814	β = 105.94
c = 62.132	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	IMAGE PLATE	RIGAKU RAXIS		2006-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	30	99.9	0.199	5	4.3		29052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07		99.2		4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB Entry: 1F6B	2	30	29010	1470	99.227	0.226	0.2238	0.23	0.2694	0.27	thin shells	18.669

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]
0.914		0.138	-1.376		0.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.112
r_dihedral_angle_4_deg	18.716
r_dihedral_angle_3_deg	12.564
r_dihedral_angle_1_deg	4.935
r_mcangle_it	3.217
r_scangle_it	3.019
r_mcbond_it	2.71
r_scbond_it	2.218
r_angle_refined_deg	1.422
r_angle_other_deg	0.953
r_mcbond_other	0.605
r_symmetry_vdw_refined	0.261
r_symmetry_vdw_other	0.205
r_nbd_refined	0.2
r_nbd_other	0.187
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.083
r_nbtor_other	0.082
r_symmetry_hbond_refined	0.066
r_bond_refined_d	0.017
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2661
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	58

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction