2G79 | pdb_00002g79

Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	30% (w/v) PEG 8000 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.493	α = 90
b = 46.325	β = 90
c = 73.597	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	77	CCD	MARRESEARCH		2004-11-27	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.000	APS	32-ID

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	1.69	50	99.6	0.076	17.03		18002	17931		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.69	1.75	99.9	99.9	0.741

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Rigid Body Refinement	THROUGHOUT	1.69	39.19	17868	17868	1815	99.4	0.161	0.161	0.155	0.17	0.214	0.22	RANDOM	21.178

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]
0.04			0.23		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.157
r_dihedral_angle_3_deg	13.498
r_dihedral_angle_4_deg	12.563
r_sphericity_free	8.352
r_dihedral_angle_1_deg	6.883
r_scangle_it	5.524
r_scbond_it	3.651
r_sphericity_bonded	3.307
r_mcangle_it	2.773
r_rigid_bond_restr	2.123
r_angle_refined_deg	1.819
r_mcbond_it	1.801
r_angle_other_deg	0.883
r_mcbond_other	0.731
r_metal_ion_refined	0.304
r_symmetry_vdw_refined	0.238
r_nbd_refined	0.222
r_symmetry_vdw_other	0.215
r_xyhbond_nbd_refined	0.21
r_nbd_other	0.202
r_xyhbond_nbd_other	0.195
r_nbtor_refined	0.178
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.117
r_nbtor_other	0.088
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1103
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	51

Software

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