3QDA | pdb_00003qda

Crystal structure of W95L beta-2 microglobulin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	19-20% PEG4000, 20% glycerol, 0.2 M ammonium acetate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.41	α = 90
b = 28.98	β = 121.77
c = 54.45	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	110	CCD	ADSC QUANTUM 4	Toroidal Zerodur mirror	2010-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.569	26.654	99.8	0.056	17	4.4	14660	14630

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	1.57	1.65	98.3		0.251	5.4	4.3	2118

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 1LDS	1.57	26.65	13895	734	99.8	0.14941	0.14698	0.1619	0.19781	0.209	RANDOM	14.342

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]
-0.03		-0.04	0.04		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.216
r_dihedral_angle_4_deg	18.585
r_dihedral_angle_3_deg	13.144
r_dihedral_angle_1_deg	7.924
r_scangle_it	3.951
r_mcangle_it	3.486
r_scbond_it	2.717
r_mcbond_it	2.362
r_angle_refined_deg	1.505
r_rigid_bond_restr	1.324
r_angle_other_deg	0.869
r_mcbond_other	0.722
r_chiral_restr	0.095
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	831
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling