3B9C | pdb_00003b9c

Crystal Structure of Human GRP CRD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X50	PDB ENTRY 1x50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	100mM Tris-HCl pH7.5, 2% PEG 400, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.14	α = 90
b = 96.67	β = 118.79
c = 61.57	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MAR CCD 165 mm		2005-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	1.0000	BSRF	3W1A

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	1.81	20	93.9	0.065	0.065	4.3	3.4	54223	49473

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)
	1.81	1.87	80.8		0.275	0.275	1	2.2	54223

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1x50	1.9	20	45293	2452	95.99	0.22357	0.22121	0.22	0.26631	0.26	RANDOM	29.702

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]
2.97		3.93	-0.88		1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.784
r_dihedral_angle_1_deg	13.98
r_dihedral_angle_3_deg	13.037
r_dihedral_angle_4_deg	11.446
r_scangle_it	2.95
r_scbond_it	1.923
r_angle_refined_deg	1.533
r_mcangle_it	1.165
r_mcbond_it	0.994
r_nbtor_refined	0.307
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.114
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4250
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
PHASER	phasing