2QQ5

Crystal structure of human SDR family member 1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AE1	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental model	PDB	1AE1	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental model	PDB	2EW8	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental model	PDB	1ZEM	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental model	PDB	1AHH	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8
experimental model	PDB	1VL8	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	2.4M Na Malonate pH 7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.225	α = 90
b = 87.854	β = 90
c = 100.583	γ = 90

Symmetry
Space Group	I 2 2 2

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 HTC	OSMIC	2007-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	22.21	99.8	0.056	0.065	17.8	3.9	91682	91499		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.567	0.66	2	3.8	12938

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8	1.8	22.21	22214	1203	99.68	0.15881	0.15681	0.19719	RANDOM	29.684

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]
0.38			-1.29		0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.662
r_dihedral_angle_4_deg	14.306
r_dihedral_angle_3_deg	10.488
r_scangle_it	6.621
r_dihedral_angle_1_deg	5.596
r_scbond_it	4.712
r_mcangle_it	3.306
r_mcbond_it	2.318
r_angle_refined_deg	1.213
r_angle_other_deg	0.918
r_mcbond_other	0.71
r_symmetry_vdw_other	0.248
r_nbd_refined	0.235
r_nbd_other	0.189
r_nbtor_refined	0.173
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.13
r_nbtor_other	0.086
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1748
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing